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- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/counts_3xtg.csv +0 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/deseq2_results_3xtg.csv +0 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/deseq2_results_5xfad.csv +0 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/execution_log.txt +0 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/kegg_3xtg.csv +327 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/kegg_5xfad.csv +342 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/kegg_enrichment.R +115 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/kegg_ps3o1s.csv +294 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/metadata_3xtg.csv +7 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/output_validation.json +17 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/pathway_comparison.csv +349 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/retrieval_plan.json +1364 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/run_metadata.json +32 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/sig_genes_5xfad.txt +2468 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/sig_genes_ps3o1s.txt +797 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/entrez_3xTgAD.txt +485 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/entrez_PS3O1S.txt +633 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/execution_log.txt +2106 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/final_answer.txt +26 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/kegg_all_pathways.csv +355 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/metadata_3xTgAD.csv +7 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/metadata_5xFAD.csv +21 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/output_validation.json +15 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv +355 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/run_metadata.json +32 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/run_summary.json +17 -0
- experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/task_query.txt +44 -0
- experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135339/decode_alphabet.R +39 -0
- experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135339/extract_model2.R +21 -0
- experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135339/inspect_rdata.R +34 -0
- experiments/bioagent_bench/runs/scale_1000/cystic-fibrosis_20260515_141940/retrieval_plan.json +0 -0
- experiments/bioagent_bench/runs/scale_1000/cystic-fibrosis_20260515_141940/run_metadata.json +32 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/anc_reference.amb +11 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/anc_reference.ann +609 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/anc_reference.fasta.fai +304 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/ancestor.raw.vcf +0 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/ancestor.sorted.bam.bai +0 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/annotate_variants.py +244 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/ecoli_reference.amb +1 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/ecoli_reference.ann +3 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/evol1.raw.vcf +0 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/evol1.sorted.bam.bai +0 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/evol2.raw.vcf +0 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/evol2.sorted.bam.bai +0 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/execution_log.json +0 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/execution_log.txt +0 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/final_answer.txt +36 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/output_validation.json +24 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/run_summary.json +22 -0
- experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/task_query.txt +47 -0
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/counts_3xtg.csv
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experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/deseq2_results_3xtg.csv
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experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/deseq2_results_5xfad.csv
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experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/execution_log.txt
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experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/kegg_3xtg.csv
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| 1 |
+
"pathway","pvalue","overlap_genes","padj"
|
| 2 |
+
"Pathways in cancer - Mus musculus (house mouse) Homo sapiens mmu05200",6.87422082517189e-24,"12444,12550,16161,12447,16001,11789,14365,56289,11863,11864,20183,218772,16775,16000,14281,22031,14165,14368,224129,15975,12575,17685,12322,16782,16780,14178,18129,18211,21802,16653,16453,53978,19225,17350,19395,12402,112407,18707,12571,72993,213498,15208,14708,12982,20315,16188,14867,240168,93897",2.24099598900603e-21
|
| 3 |
+
"Neuroactive ligand signaling - Mus musculus (house mouse) Homo sapiens mmu04082",1.40968724580365e-18,"216227,11540,14399,13488,12647,224129,108068,63993,14680,18387,14400,21336,14412,14411,14812,13489,22348,17201,11553,18619,11549,14708,108073,14811,21333,15552,20508",2.16436511616009e-16
|
| 4 |
+
"PI3K-Akt signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04151",2.38167983080449e-18,"12444,12447,16001,21960,12189,16775,20393,16000,14165,14573,12824,15975,15370,12575,170755,16782,16780,14178,12841,18211,75778,20750,21802,16653,11601,13685,16453,53978,18707,21825,12571,14708,16542,16188,213119",2.16436511616009e-16
|
| 5 |
+
"Neuroactive ligand-receptor interaction - Mus musculus (house mouse) Homo sapiens mmu04080",2.65566271921484e-18,"237213,22353,11540,14399,13488,108068,14652,11516,14419,18387,71897,14400,21336,14812,11535,53978,13489,12424,70086,18166,17201,20607,11553,14293,18619,11549,20606,14289,108073,14811,21333,58991,15552,381073,14804,14294",2.16436511616009e-16
|
| 6 |
+
"Human papillomavirus infection - Mus musculus (house mouse) Homo sapiens mmu05165",5.12298833915413e-17,"12444,12447,11789,14365,21960,16775,19164,22031,14368,12824,15975,12575,19106,66237,240095,16782,16780,12841,18129,20750,16653,13685,19225,18707,21825,12571,56489,15208,15018,110557,100529082,93897,213119",3.34018839712849e-15
|
| 7 |
+
"Cadherin signaling - Mus musculus (house mouse) Homo sapiens mmu04519",6.15182387610664e-16,"12550,16001,11789,14365,12614,216965,353499,19164,14399,268482,14368,22352,14400,11461,16653,72088,12555,219228,66809,93883,93892,93885,93878,93874,93880,93882,93872,93877,239096,19049,16542,14107,93893,93897",3.34249097268461e-14
|
| 8 |
+
"cAMP signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04024",3.9684733451919e-15,"12789,22353,11540,14281,13488,224129,23984,14652,11516,12322,18160,14812,13489,18018,18166,16526,12326,18707,54611,20606,243270,14811,19049,58991,15552",1.84817472933223e-13
|
| 9 |
+
"Hormone signaling - Mus musculus (house mouse) Homo sapiens mmu04081",2.32786728148106e-14,"16001,22353,16000,13488,12166,224129,110542,14652,18387,53945,18160,13489,12424,17201,18707,72993,56089,20607,11553,18619,11549,20606,14708,58991",9.48605917203533e-13
|
| 10 |
+
"MAPK signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04010",6.0417579175502e-14,"26400,16001,56808,216965,67603,16000,14281,14165,14573,15370,19252,26405,14178,18211,17165,21802,16653,11601,320139,19395,18018,329502,16542,54376,78390,240168,211429",2.18845897902374e-12
|
| 11 |
+
"Calcium signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04020",7.91989062264887e-14,"18575,94178,11540,13488,14165,14573,18574,14680,12322,14178,228550,18211,21802,21336,14812,114875,18018,70086,12326,11549,20192,14811,16542,73333,110893",2.58188434298353e-12
|
| 12 |
+
"Oxytocin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04921",1.20785746333224e-13,"56808,14281,224129,12575,12322,18160,11461,16653,19225,18018,60596,12326,108097,234889,329502,20192,211480,54376,78390,211429",3.29971303163086e-12
|
| 13 |
+
"Ras signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04014",1.21461829385185e-13,"16001,56289,16000,20418,14165,11352,14178,18211,21802,14812,16653,18481,11601,19395,18707,53357,14708,329502,14811,16542,78390,240168,214230,211429",3.29971303163086e-12
|
| 14 |
+
"Motor proteins - Mus musculus (house mouse) Homo sapiens mmu04814",1.89698131781588e-13,"100040563,67951,16568,56427,67665,21956,13427,109242,11461,13417,320191,244281,227058,381917,330355,17885,21955,21647,100041639,100310872,100040531,21648",4.7570454585229e-12
|
| 15 |
+
"Epstein-Barr virus infection - Mus musculus (house mouse) Homo sapiens mmu05169",3.86229482659999e-13,"12444,12447,26400,14128,12503,22031,15975,12575,19106,240095,22352,16453,14960,15894,18707,12571,56489,15018,12010,23960,110557,14961,100529082",8.99362938193997e-12
|
| 16 |
+
"Ascorbate and aldarate metabolism - Mus musculus (house mouse) Homo sapiens mmu00053",4.90218544646341e-13,"11669,110695,94284,613123,394433,394436,394432,394435,394430,22236,394434",1.06540830369805e-11
|
| 17 |
+
"Chemical carcinogenesis - receptor activation - Mus musculus (house mouse) Homo sapiens mmu05207",5.58126569924988e-13,"16600,11863,20183,14281,14165,224129,14178,18129,16653,13685,18707,56489,94284,723963,14867,613123,394433,394436,394432,394435,394430,22236,394434",1.13718288622216e-11
|
| 18 |
+
"Cytoskeleton in muscle cells - Mus musculus (house mouse) Homo sapiens mmu04820",6.69002484639522e-13,"14114,13003,24131,18074,21956,22352,12831,12841,12814,15530,11461,70435,233199,21825,118449,11472,17885,319565,14115,21955,640524,12335,213119",1.28291064701461e-11
|
| 19 |
+
"Integrin signaling - Mus musculus (house mouse) Homo sapiens mmu04518",1.11294244580784e-12,"12444,12550,16001,21960,16775,16000,12824,16782,16780,241639,12841,20750,11461,231470,15894,18707,21825,16542,213119",2.01566242962975e-11
|
| 20 |
+
"Retinol metabolism - Mus musculus (house mouse) Homo sapiens mmu00830",1.7305335489919e-12,"108841,19378,26358,19892,11668,94284,232174,19683,613123,394433,394436,394432,394435,394430,22236,394434",2.96923124721767e-11
|
| 21 |
+
"Human T-cell leukemia virus 1 infection - Mus musculus (house mouse) Homo sapiens mmu05166",1.90999104316981e-12,"12444,12447,30939,14281,224129,12575,12504,240095,16653,16453,18018,14960,15894,13654,13653,18707,12236,15018,12010,73333,110557,14961,100529082",3.11328540036678e-11
|
| 22 |
+
"Metabolism of xenobiotics by cytochrome P450 - Mus musculus (house mouse) Homo sapiens mmu00980",4.32246355996308e-12,"15483,77337,109857,13106,94284,14867,613123,394433,394436,394432,394435,394430,22236,394434",6.71011009784745e-11
|
| 23 |
+
"Rap1 signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04015",7.4109425224617e-12,"12550,16001,16000,11540,14165,224129,14178,11461,14812,16653,11601,53978,13489,19395,18707,21825,15901,14293,14811,16542,240168",1.09816693741932e-10
|
| 24 |
+
"Drug metabolism - other enzymes - Mus musculus (house mouse) Homo sapiens mmu00983",9.03191504757962e-12,"22271,13106,54369,103149,94284,14867,613123,394433,394436,394432,394435,394430,22236,394434,436059",1.28017578500476e-10
|
| 25 |
+
"Kaposi sarcoma-associated herpesvirus infection - Mus musculus (house mouse) Homo sapiens mmu05167",1.49287526318892e-11,"26400,14281,22031,15975,12575,19106,240095,12768,16653,11601,19225,18018,74603,15894,18707,12571,56489,14708,15018,110557,100529082",2.02782223249828e-10
|
| 26 |
+
"Focal adhesion - Mus musculus (house mouse) Homo sapiens mmu04510",1.97156474730488e-11,"12444,16001,21960,16775,16000,20418,12824,13731,16782,16780,12841,20750,11461,13730,18481,18707,21825,16542,214230,213119",2.57092043048556e-10
|
| 27 |
+
"Signaling pathways regulating pluripotency of stem cells - Mus musculus (house mouse) Homo sapiens mmu04550",2.44421238816576e-11,"16600,16001,11789,14365,16000,17268,15904,12166,14368,13395,16653,16453,11906,18707,16392,15901,93897",3.06466630208476e-10
|
| 28 |
+
"Drug metabolism - cytochrome P450 - Mus musculus (house mouse) Homo sapiens mmu00982",3.28029621794767e-11,"13106,109731,55990,94284,14867,613123,394433,394436,394432,394435,394430,22236,394434",3.96065395204052e-10
|
| 29 |
+
"Breast cancer - Mus musculus (house mouse) Homo sapiens mmu05224",5.36264355446968e-11,"16001,11789,14365,12189,16000,14281,20418,14165,14368,12575,14178,18129,16653,18707,12571,15208,93897",6.24364928127541e-10
|
| 30 |
+
"Osteoclast differentiation - Mus musculus (house mouse) Homo sapiens mmu04380",9.62160268854905e-11,"26400,14282,14281,15975,14130,13038,18726,18018,74256,12326,18707,16477,232790,18733,14728,18725",1.08160085395413e-09
|
| 31 |
+
"ErbB signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04012",2.47038967705525e-10,"26400,20418,12575,15200,12322,11352,21802,16653,18481,13685,12402,18707,214230",2.62297395601244e-09
|
| 32 |
+
"Alcoholism - Mus musculus (house mouse) Homo sapiens mmu05034",2.49423903792594e-10,"14282,15081,11540,20418,13488,224129,63959,14812,16653,13489,12326,109731,14708,14811,232440,19049,319190,319176,319162",2.62297395601244e-09
|
| 33 |
+
"Efferocytosis - Mus musculus (house mouse) Homo sapiens mmu04148",2.76411659142866e-10,"18263,11303,11863,20393,50769,19128,12322,22174,19225,18018,320091,21825,53357,12642,497097,70676,320940",2.81594377751795e-09
|
| 34 |
+
"Human immunodeficiency virus 1 infection - Mus musculus (house mouse) Homo sapiens mmu05170",4.67749145654413e-10,"26400,12503,80287,14281,12504,240095,21938,16653,18481,18018,18707,14708,319236,209387,667823,15018,12010,110557,214230,100529082",4.6207945904042e-09
|
| 35 |
+
"Chemical carcinogenesis - DNA adducts - Mus musculus (house mouse) Homo sapiens mmu05204",5.99291367967882e-10,"15483,13106,19225,94284,14867,613123,394433,394436,394432,394435,394430,22236,394434",5.7461466458097e-09
|
| 36 |
+
"FoxO signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04068",1.0239437527307e-09,"12444,26558,16001,20528,20393,16000,20620,12575,170755,12359,16653,108097,18707,213393,329934",9.5373046682917e-09
|
| 37 |
+
"Porphyrin metabolism - Mus musculus (house mouse) Homo sapiens mmu00860",1.12587520988957e-09,"11656,94284,613123,394433,394436,394432,394435,394430,22236,394434",1.01954255117778e-08
|
| 38 |
+
"Cocaine addiction - Mus musculus (house mouse) Homo sapiens mmu05030",1.40383459786205e-09,"14282,19739,13488,224129,108068,14812,13489,109731,14811,19049",1.21687523548198e-08
|
| 39 |
+
"mTOR signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04150",1.41844352602195e-09,"16001,14365,17254,20393,16000,14245,14368,66237,52187,16653,13685,18707,20539,252875,268706,93897",1.21687523548198e-08
|
| 40 |
+
"Pentose and glucuronate interconversions - Mus musculus (house mouse) Homo sapiens mmu00040",2.14290481915033e-09,"94284,613123,394433,394436,394432,394435,394430,22236,394434",1.79124864370002e-08
|
| 41 |
+
"Steroid hormone biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00140",2.5737254480782e-09,"15483,77337,13106,13075,94284,613123,394433,394436,394432,394435,394430,22236,394434",2.09177069922021e-08
|
| 42 |
+
"Cytokine-cytokine receptor interaction - Mus musculus (house mouse) Homo sapiens mmu04060",2.63075456036898e-09,"16161,237313,12166,15975,110542,20300,12504,12768,16182,21938,21941,12160,12458,12982,20315,16188,20301,14559,100862177,100504239,100040048",2.09177069922021e-08
|
| 43 |
+
"Glycerophospholipid metabolism - Mus musculus (house mouse) Homo sapiens mmu00564",2.91098841073418e-09,"50767,14245,19012,12647,14555,77582,320127,53357,215456,329502,78390,28042,211429",2.25948148071272e-08
|
| 44 |
+
"Pathways of neurodegeneration - multiple diseases - Mus musculus (house mouse) Homo sapiens mmu05022",3.04218091842835e-09,"67951,26400,75512,11789,14365,19164,14368,50873,67665,12322,12359,21938,170731,14812,16653,19225,13417,66091,227058,52639,78174,381917,330355,20192,14811,73333,93897",2.3063976265294e-08
|
| 45 |
+
"Gastric cancer - Mus musculus (house mouse) Homo sapiens mmu05226",5.46266400205827e-09,"12550,12447,11789,14365,20183,218772,20418,14165,14368,12575,14178,16653,17350,18707,93897",4.04733741970681e-08
|
| 46 |
+
"ECM-receptor interaction - Mus musculus (house mouse) Homo sapiens mmu04512",6.12755312323701e-09,"21960,16775,12824,16782,16780,12841,15530,20750,231470,21825,75209,213119",4.43907181816725e-08
|
| 47 |
+
"Hepatocellular carcinoma - Mus musculus (house mouse) Homo sapiens mmu05225",6.27462508423112e-09,"16001,11789,14365,70127,20418,14368,83797,12575,67155,11461,21802,16653,18707,12571,14867,93897",4.44679951621597e-08
|
| 48 |
+
"Proteoglycans in cancer - Mus musculus (house mouse) Homo sapiens mmu05205",8.65683380007442e-09,"16001,14365,16000,14368,12575,15200,12322,15530,11461,16653,12402,18707,21825,22350,16542,545291,93897",6.00452727409417e-08
|
| 49 |
+
"Small cell lung cancer - Mus musculus (house mouse) Homo sapiens mmu05222",1.1544118019059e-08,"12447,20183,218772,16775,22031,12575,16782,16780,19225,18707,12571,14198",7.84038015461088e-08
|
| 50 |
+
"Herpes simplex virus 1 infection - Mus musculus (house mouse) Homo sapiens mmu05168",1.24286012962292e-08,"22031,15975,19106,240095,16149,18986,13685,14960,18707,56489,245610,15018,12010,23960,110557,14961,100529082",8.26882453585858e-08
|
| 51 |
+
"Choline metabolism in cancer - Mus musculus (house mouse) Homo sapiens mmu05231",1.86332482192639e-08,"14281,19012,20519,63993,16653,13685,320127,18707,20518,329502,78390,211429",1.214887783896e-07
|
| 52 |
+
"Alcoholic liver disease - Mus musculus (house mouse) Homo sapiens mmu04936",1.91931367862716e-08,"26400,107476,14245,22031,13106,11669,101214,20249,108097,100705,56489,329065,110695,12268",1.22685541025972e-07
|
| 53 |
+
"Measles - Mus musculus (house mouse) Homo sapiens mmu05162",2.1012403646219e-08,"12444,12447,14281,22031,15975,19106,14130,22062,170786,16453,18707,12571,56489,23960",1.30769042565453e-07
|
| 54 |
+
"B cell receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04662",2.12599977176964e-08,"14281,14130,16653,18726,12483,18018,18707,18733,14728,240168,18725",1.30769042565453e-07
|
| 55 |
+
"Bile secretion - Mus musculus (house mouse) Homo sapiens mmu04976",2.62884922510591e-08,"224129,28250,94284,28254,613123,394433,394436,394432,394435,394430,22236,394434",1.58704601367505e-07
|
| 56 |
+
"Chemokine signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04062",2.72099465176671e-08,"14773,20418,224129,20300,12768,16653,16453,19395,18707,12458,14708,20315,20301,100862177,100504239,100040048",1.61280773904718e-07
|
| 57 |
+
"Antigen processing and presentation - Mus musculus (house mouse) Homo sapiens mmu04612",4.59056883902028e-08,"12504,240095,16149,65972,19727,14960,15018,12010,110557,14961,100529082",2.67236685985824e-07
|
| 58 |
+
"Fanconi anemia pathway - Mus musculus (house mouse) Homo sapiens mmu03460",5.22729753638275e-08,"21975,114714,68240,12189,80905,17350,26447,193838,18861",2.98964736291364e-07
|
| 59 |
+
"Amphetamine addiction - Mus musculus (house mouse) Homo sapiens mmu05031",5.56013039451753e-08,"14282,14281,13488,224129,12322,14812,12326,109731,14811,19049",3.12517673898744e-07
|
| 60 |
+
"Wnt signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04310",5.94144665142164e-08,"12444,11789,14365,12614,19164,14160,68339,14368,12322,18018,407821,494504,93897,408191,408192",3.22818601393909e-07
|
| 61 |
+
"Cell adhesion molecule (CAM) interaction - Mus musculus (house mouse) Homo sapiens mmu04514",5.94144665142164e-08,"12550,13003,17968,12504,240095,12483,12555,171486,14960,15894,66797,15018,110557,14961,100529082",3.22818601393909e-07
|
| 62 |
+
"Arachidonic acid metabolism - Mus musculus (house mouse) Homo sapiens mmu00590",6.58998183805879e-08,"19215,11688,109857,13106,15446,19225,11686,53357,329502,78390,211429",3.52185914624126e-07
|
| 63 |
+
"Cellular senescence - Mus musculus (house mouse) Homo sapiens mmu04218",6.88212606944268e-08,"12444,12447,63873,12575,240095,16653,13685,18018,18707,12571,15018,15258,73333,110557,100529082",3.61866628812631e-07
|
| 64 |
+
"Purine metabolism - Mus musculus (house mouse) Homo sapiens mmu00230",8.07093548012561e-08,"18575,229589,18574,224129,23984,225600,18160,54369,60596,234889,54611,14198,78600",4.17638883574754e-07
|
| 65 |
+
"Non-small cell lung cancer - Mus musculus (house mouse) Homo sapiens mmu05223",8.43429766505529e-08,"56289,20183,218772,12575,21802,16653,16453,18707,12571,14198",4.29622037313754e-07
|
| 66 |
+
"IgSF CAM signaling - Mus musculus (house mouse) Homo sapiens mmu04517",9.94626792586136e-08,"12550,67951,17756,17968,14270,11461,18481,170786,71566,15894,66797,18707,16490,116837,22350,16542,210801,640524,214230",4.98843591358585e-07
|
| 67 |
+
"Hematopoietic cell lineage - Mus musculus (house mouse) Homo sapiens mmu04640",1.04423216192305e-07,"14128,12504,12516,12483,12509,14960,16790,14934,12982,16188,14961",5.02789946373217e-07
|
| 68 |
+
"Morphine addiction - Mus musculus (house mouse) Homo sapiens mmu05032",1.04423216192305e-07,"14773,18575,14399,13488,18574,224129,23984,14400,22348,54611,14708",5.02789946373217e-07
|
| 69 |
+
"Serotonergic synapse - Mus musculus (house mouse) Homo sapiens mmu04726",1.04876430531837e-07,"11688,224129,19252,14400,16653,19225,11686,109731,14708,329502,15552,78390,211429",5.02789946373217e-07
|
| 70 |
+
"Parathyroid hormone synthesis, secretion and action - Mus musculus (house mouse) Homo sapiens mmu04928",1.24613161304067e-07,"20183,20393,14281,224129,12575,15200,23948,69847,13653,279561,213498,232341",5.84122770547253e-07
|
| 71 |
+
"Glioma - Mus musculus (house mouse) Homo sapiens mmu05214",1.25425134780085e-07,"16001,16000,20418,12575,12322,21802,16653,12326,18707,12571",5.84122770547253e-07
|
| 72 |
+
"Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse) Homo sapiens mmu04061",1.30311153570522e-07,"237313,20300,12768,16182,21938,12458,20315,20301,100862177,100504239,100040048",5.98330085408311e-07
|
| 73 |
+
"Salmonella infection - Mus musculus (house mouse) Homo sapiens mmu05132",1.78858913012443e-07,"100040563,67951,66616,26400,53413,14281,67665,17281,13427,11461,18481,12306,268973,18707,100310872,100040531,21648",8.09833411695228e-07
|
| 74 |
+
"Vascular smooth muscle contraction - Mus musculus (house mouse) Homo sapiens mmu04270",1.88278106716486e-07,"11540,224129,18160,11535,60596,56089,234889,213498,53357,11549,329502,78390,211429",8.35135859537475e-07
|
| 75 |
+
"Long-term depression - Mus musculus (house mouse) Homo sapiens mmu04730",1.89570716582126e-07,"16001,16000,16653,60596,234889,329502,78390,14804,211429",8.35135859537475e-07
|
| 76 |
+
"Neurotrophin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04722",1.98601938009334e-07,"26400,19164,20418,170936,12322,18211,22062,16653,77480,12326,18707,14570",8.63256423880574e-07
|
| 77 |
+
"Lysosome biogenesis - Mus musculus (house mouse) Homo sapiens mmu04142",2.11718076319893e-07,"72368,13034,94178,18457,11782,63959,66237,11777,229445,13038,52187,11605,11593,76524,15932,320528,268706",8.96364842601106e-07
|
| 78 |
+
"Human cytomegalovirus infection - Mus musculus (house mouse) Homo sapiens mmu05163",2.11718076319893e-07,"224129,12575,240095,12768,16653,13685,19225,18018,18707,12571,213498,14708,15018,12010,20315,110557,100529082",8.96364842601106e-07
|
| 79 |
+
"Circadian entrainment - Mus musculus (house mouse) Homo sapiens mmu04713",2.21468808502379e-07,"18626,14281,224129,11516,12322,14812,60596,234889,14708,20192,14811",9.25626045791994e-07
|
| 80 |
+
"MicroRNAs in cancer - Mus musculus (house mouse) Homo sapiens mmu05206",2.44506698880868e-07,"12444,12447,11789,14365,56289,21960,12189,12575,22352,18129,16653,19225,18707,171543,21825,12571,22350,387230,723963",1.00897701057168e-06
|
| 81 |
+
"Glycerolipid metabolism - Mus musculus (house mouse) Homo sapiens mmu00561",2.92060447631715e-07,"14245,19012,11669,67800,11605,320127,215456,110695,16891",1.19014632409924e-06
|
| 82 |
+
"Type I diabetes mellitus - Mus musculus (house mouse) Homo sapiens mmu04940",3.84498068039579e-07,"240095,14417,14960,15018,15893,14415,110557,14961,100529082",1.54748605161608e-06
|
| 83 |
+
"GnRH signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04912",7.1312991110613e-07,"26400,224129,26405,15200,12322,16653,13653,329502,78390,211429",2.80096808458552e-06
|
| 84 |
+
"Longevity regulating pathway - Mus musculus (house mouse) Homo sapiens mmu04211",7.1312991110613e-07,"16001,16000,224129,12359,16653,13685,12326,108097,18707,72993",2.80096808458552e-06
|
| 85 |
+
"Cushing syndrome - Mus musculus (house mouse) Homo sapiens mmu04934",7.32263721136587e-07,"214162,12447,11789,14365,11863,14368,224129,15370,12575,12322,16526,12571,93897",2.81411812239325e-06
|
| 86 |
+
"Renal cell carcinoma - Mus musculus (house mouse) Homo sapiens mmu05211",7.33742455225235e-07,"11863,11864,12575,21802,16653,18481,112407,18707,214230",2.81411812239325e-06
|
| 87 |
+
"Cholinergic synapse - Mus musculus (house mouse) Homo sapiens mmu04725",8.38724348632934e-07,"14281,12647,224129,63993,12322,16653,12326,18707,14708,211480,20508",3.15441371585486e-06
|
| 88 |
+
"Hepatitis B - Mus musculus (house mouse) Homo sapiens mmu05161",8.4182206527415e-07,"12447,26400,14281,22031,15975,12575,15530,16653,16453,18018,13654,18707,56489",3.15441371585486e-06
|
| 89 |
+
"Melanoma - Mus musculus (house mouse) Homo sapiens mmu05218",9.36034829627951e-07,"12550,16001,16000,14165,12575,14178,16653,18707,12571",3.46758357339445e-06
|
| 90 |
+
"Glutamatergic synapse - Mus musculus (house mouse) Homo sapiens mmu04724",1.08769061586757e-06,"26558,216227,224129,108068,14812,14708,329502,108073,14811,78390,211429",3.98412517722277e-06
|
| 91 |
+
"Viral carcinogenesis - Mus musculus (house mouse) Homo sapiens mmu05203",1.19637793518929e-06,"12444,12447,22031,12575,19106,240095,16653,16453,13654,18707,12571,15018,319190,110557,100529082",4.33354674301897e-06
|
| 92 |
+
"Influenza A - Mus musculus (house mouse) Homo sapiens mmu05164",1.64005074388222e-06,"22031,15975,19106,11461,14960,15894,18707,12571,56489,245610,23960,73333,14961",5.87534662094068e-06
|
| 93 |
+
"Phospholipase D signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04072",1.86661677192342e-06,"20418,19012,224129,108068,16653,53978,320127,18707,329502,108073,78390,211429",6.61431595268515e-06
|
| 94 |
+
"Necroptosis - Mus musculus (house mouse) Homo sapiens mmu04217",1.98489034204685e-06,"15975,19106,12322,16453,74256,263876,329502,232440,319176,73333,78390,319162,211429",6.95778765061584e-06
|
| 95 |
+
"AMPK signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04152",2.44895136776224e-06,"16001,20528,16000,107476,13685,20249,108097,18707,100705,11549,329065",8.49317176479246e-06
|
| 96 |
+
"Phagosome - Mus musculus (house mouse) Homo sapiens mmu04145",2.54420283555379e-06,"67951,66237,240095,14130,13427,11461,170786,14960,21825,15018,110557,14961,100529082",8.63968879573474e-06
|
| 97 |
+
"Axon guidance - Mus musculus (house mouse) Homo sapiens mmu04360",2.54420283555379e-06,"14365,12322,226251,14270,20348,16653,18481,237860,18707,22067,20315,210801,214230",8.63968879573474e-06
|
| 98 |
+
"Inflammatory mediator regulation of TRP channels - Mus musculus (house mouse) Homo sapiens mmu04750",3.07754647300385e-06,"63873,16000,224129,11419,12322,18211,18707,53357,329502,78390,211429",1.03430943319511e-05
|
| 99 |
+
"Hippo signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04390",3.44529948658125e-06,"12444,12550,11789,14365,56289,12166,14368,22062,11461,12160,15901,93897",1.14608942104642e-05
|
| 100 |
+
"Ovarian steroidogenesis - Mus musculus (house mouse) Homo sapiens mmu04913",3.77138066878303e-06,"16001,16000,224129,13075,19225,329502,78390,211429",1.24188898790229e-05
|
| 101 |
+
"Transcriptional misregulation in cancer - Mus musculus (house mouse) Homo sapiens mmu05202",4.15423660675825e-06,"12444,214162,16001,11864,20183,15081,67603,16000,17268,12575,18211,15446,16909,58208",1.35428113380319e-05
|
| 102 |
+
"Dopaminergic synapse - Mus musculus (house mouse) Homo sapiens mmu04728",5.11970540410671e-06,"14281,13488,224129,14680,12322,14812,13489,109731,14708,14811,19049",1.62110766123671e-05
|
| 103 |
+
"Th1 and Th2 cell differentiation - Mus musculus (house mouse) Homo sapiens mmu04658",5.12190457384604e-06,"16161,12503,14281,12504,18129,16453,18018,14960,14961",1.62110766123671e-05
|
| 104 |
+
"Colorectal cancer - Mus musculus (house mouse) Homo sapiens mmu05210",5.12190457384604e-06,"11789,14281,12575,17685,21802,16653,17350,18707,72993",1.62110766123671e-05
|
| 105 |
+
"beta-Alanine metabolism - Mus musculus (house mouse) Homo sapiens mmu00410",5.61891927179982e-06,"14417,11669,103149,110695,73748,14415",1.76131507942956e-05
|
| 106 |
+
"Insulin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04910",6.30635034948743e-06,"20528,216019,107476,53413,20418,16653,13685,12402,108097,18707,100705",1.95797163231705e-05
|
| 107 |
+
"GABAergic synapse - Mus musculus (house mouse) Homo sapiens mmu04727",6.7623208252869e-06,"14399,224129,14417,14400,14412,14411,22348,14708,14415",2.07973263117314e-05
|
| 108 |
+
"Chemical carcinogenesis - reactive oxygen species - Mus musculus (house mouse) Homo sapiens mmu05208",6.9347563678937e-06,"26400,11863,77337,14281,13106,11352,12359,16653,66091,18707,11431,78174,14867,73333",2.1128323139564e-05
|
| 109 |
+
"Viral myocarditis - Mus musculus (house mouse) Homo sapiens mmu05416",7.4005993646742e-06,"240095,11352,11461,14960,15894,15018,110557,14961,100529082",2.23388462304055e-05
|
| 110 |
+
"HIF-1 signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04066",7.85232961048837e-06,"16001,11863,16000,216019,12575,12322,11601,13685,112407,18707",2.32714495729019e-05
|
| 111 |
+
"Growth hormone synthesis, secretion and action - Mus musculus (house mouse) Homo sapiens mmu04935",7.85232961048837e-06,"16000,14281,20418,224129,16653,18707,20607,20606,16477,58991",2.32714495729019e-05
|
| 112 |
+
"TNF signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04668",8.46976482652652e-06,"26400,14281,22031,16182,21938,19225,74256,15894,18707,16477",2.4875165166195e-05
|
| 113 |
+
"Regulation of actin cytoskeleton - Mus musculus (house mouse) Homo sapiens mmu04810",8.86410338019016e-06,"23920,11789,14165,14178,11461,16653,18481,53978,237860,18707,22350,20315,214230,213119",2.58008723387678e-05
|
| 114 |
+
"Tryptophan metabolism - Mus musculus (house mouse) Homo sapiens mmu00380",9.27465152904013e-06,"21743,209692,12359,11669,15930,109731,110695",2.67569592784698e-05
|
| 115 |
+
"Endocytosis - Mus musculus (house mouse) Homo sapiens mmu04144",9.55263587318523e-06,"14773,16001,66313,216724,57440,30948,240095,67588,69178,12402,215445,78618,15018,110557,100529082",2.7317186795249e-05
|
| 116 |
+
"Arginine and proline metabolism - Mus musculus (house mouse) Homo sapiens mmu00330",1.19759819253297e-05,"19125,18263,11669,109731,320452,110695,100041585",3.3949305283978e-05
|
| 117 |
+
"Systemic lupus erythematosus - Mus musculus (house mouse) Homo sapiens mmu05322",1.2164244685538e-05,"15081,20822,14812,14960,14811,232440,319190,319176,12268,14961,319162",3.39923270916529e-05
|
| 118 |
+
"Oocyte meiosis - Mus musculus (house mouse) Homo sapiens mmu04114",1.22262951093347e-05,"12447,56739,16001,67141,16000,30939,224129,268930,12322,114875",3.39923270916529e-05
|
| 119 |
+
"Parkinson disease - Mus musculus (house mouse) Homo sapiens mmu05012",1.24120376659142e-05,"67951,11540,13488,224129,50873,19252,14680,12322,170731,13489,66091,109731,78174,20192,73333",3.39923270916529e-05
|
| 120 |
+
"p53 signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04115",1.25125130398722e-05,"12444,12447,16000,12575,22401,22062,21825,12571",3.39923270916529e-05
|
| 121 |
+
"Renin secretion - Mus musculus (house mouse) Homo sapiens mmu04924",1.25125130398722e-05,"18575,18574,224129,11516,18160,60596,234889,54611",3.39923270916529e-05
|
| 122 |
+
"African trypanosomiasis - Mus musculus (house mouse) Homo sapiens mmu05143",1.35612174708385e-05,"16775,15930,15894,110257,15122,101488143",3.65368338470525e-05
|
| 123 |
+
"Synaptic vesicle cycle - Mus musculus (house mouse) Homo sapiens mmu04721",1.52175684318274e-05,"216227,66237,14412,14411,22348,116837,208898,20508",4.06633385965224e-05
|
| 124 |
+
"Alzheimer disease - Mus musculus (house mouse) Homo sapiens mmu05010",1.74602901806789e-05,"67951,26400,11789,14365,19164,14368,19106,14812,16653,19225,66091,18707,52639,78174,20192,14811,73333,93897",4.62768666577343e-05
|
| 125 |
+
"VEGF signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04370",1.9346414365785e-05,"16653,19225,18707,329502,16542,78390,211429",5.08623474455316e-05
|
| 126 |
+
"Staphylococcus aureus infection - Mus musculus (house mouse) Homo sapiens mmu05150",2.12101835625704e-05,"268482,14130,66809,14960,15894,14293,14289,12268,14961,14294",5.53161587311837e-05
|
| 127 |
+
"Nicotine addiction - Mus musculus (house mouse) Homo sapiens mmu05033",2.15859637277815e-05,"216227,14399,14400,14812,22348,14811",5.56811905433828e-05
|
| 128 |
+
"Th17 cell differentiation - Mus musculus (house mouse) Homo sapiens mmu04659",2.16917521442013e-05,"16161,12503,20183,14281,12504,16453,18018,14960,14961",5.56811905433828e-05
|
| 129 |
+
"Bladder cancer - Mus musculus (house mouse) Homo sapiens mmu05219",2.4980011097082e-05,"12550,56289,12575,15200,16653,21825",6.36209657628807e-05
|
| 130 |
+
"Prostate cancer - Mus musculus (house mouse) Homo sapiens mmu05215",2.52309427369761e-05,"53320,12447,16001,23920,16000,12575,21802,16653,18707",6.37619173042963e-05
|
| 131 |
+
"Longevity regulating pathway - multiple species - Mus musculus (house mouse) Homo sapiens mmu04213",2.704475173833e-05,"16001,16000,224129,12359,16653,108097,18707",6.76305818207946e-05
|
| 132 |
+
"Protein digestion and absorption - Mus musculus (house mouse) Homo sapiens mmu04974",2.71767061917917e-05,"140709,17254,50934,12824,12831,12841,12814,213945,110893",6.76305818207946e-05
|
| 133 |
+
"Viral life cycle - HIV-1 - Mus musculus (house mouse) Homo sapiens mmu03250",3.3456877463893e-05,"80287,12504,269344,17755,319236,209387,667823",8.26283488880994e-05
|
| 134 |
+
"Gap junction - Mus musculus (house mouse) Homo sapiens mmu04540",3.42626335844048e-05,"67951,13488,224129,26405,16653,13489,60596,234889",8.39820943497442e-05
|
| 135 |
+
"Amyotrophic lateral sclerosis - Mus musculus (house mouse) Homo sapiens mmu05014",3.68966062722995e-05,"67951,75512,50873,67665,12359,21938,11461,14812,13417,66091,227058,52639,78174,381917,330355,245610,14811",8.97633854087287e-05
|
| 136 |
+
"Apelin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04371",3.75859001886932e-05,"12550,224129,20750,16653,12326,108097,13653,14708,20192,110893",9.07629886038072e-05
|
| 137 |
+
"Malaria - Mus musculus (house mouse) Homo sapiens mmu05144",4.53741109174724e-05,"170733,15894,21825,14934,110257,15122,101488143",0.00010876441293453
|
| 138 |
+
"Thermogenesis - Mus musculus (house mouse) Homo sapiens mmu04714",4.72102802988879e-05,"70127,224129,83797,73694,67155,69487,18160,11461,16653,231430,66091,108097,78174",0.000112339791076186
|
| 139 |
+
"Adherens junction - Mus musculus (house mouse) Homo sapiens mmu04520",5.57380857062211e-05,"12550,216527,16001,66313,19263,11461,69903,11431",0.000131671130001653
|
| 140 |
+
"Fluid shear stress and atherosclerosis - Mus musculus (house mouse) Homo sapiens mmu05418",6.37290924339265e-05,"26400,63873,14281,12166,19252,11461,15894,18707,16542,14867",0.00014946535347813
|
| 141 |
+
"Fc gamma R-mediated phagosome formation - Mus musculus (house mouse) Homo sapiens mmu04666",6.50030771925069e-05,"19012,30948,14130,18707,53357,329502,78390,211429",0.000151364308319695
|
| 142 |
+
"Ether lipid metabolism - Mus musculus (house mouse) Homo sapiens mmu00565",7.0477468159688e-05,"19012,53357,329502,78390,28042,211429",0.000162843510010836
|
| 143 |
+
"T cell receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04660",7.09318356488919e-05,"26400,12503,14281,12504,16653,18481,18018,18707,214230",0.000162843510010836
|
| 144 |
+
"Lipid and atherosclerosis - Mus musculus (house mouse) Homo sapiens mmu05417",8.11012722649304e-05,"26400,11303,20183,14281,22031,12322,18986,16653,18018,15894,18707,56489",0.000184888215093478
|
| 145 |
+
"Retrograde endocannabinoid signaling - Mus musculus (house mouse) Homo sapiens mmu04723",8.40090547854639e-05,"216227,14399,224129,14400,19225,66091,22348,231871,116837,14708",0.00019018716569487
|
| 146 |
+
"Virion - Ebolavirus, Lyssavirus and Morbillivirus - Mus musculus (house mouse) Homo sapiens mmu03265",8.58121914967601e-05,"11889,17968,14130,170786",0.000192929478813405
|
| 147 |
+
"Platelet activation - Mus musculus (house mouse) Homo sapiens mmu04611",9.1024502164734e-05,"224129,11461,19395,60596,18707,234889,329502,78390,211429",0.000203246491134954
|
| 148 |
+
"Ubiquitin mediated proteolysis - Mus musculus (house mouse) Homo sapiens mmu04120",9.3528997746854e-05,"12189,66313,50873,59026,15204,12402,17318,231380,67455,218793",0.000207418049424996
|
| 149 |
+
"Cell cycle - Mus musculus (house mouse) Homo sapiens mmu04110",9.86216186883424e-05,"12444,12447,67141,30939,19090,12575,268930,76464,12236,12571",0.000217234106029727
|
| 150 |
+
"Hypertrophic cardiomyopathy - Mus musculus (house mouse) Homo sapiens mmu05410",0.000100783172927684,"56808,16000,21956,11461,108097,54376,110893,213119",0.000220505465600168
|
| 151 |
+
"Dilated cardiomyopathy - Mus musculus (house mouse) Homo sapiens mmu05414",0.000124014168176359,"56808,16000,224129,21956,11461,54376,110893,213119",0.000269524125503287
|
| 152 |
+
"Toll-like receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04620",0.000132674806945946,"26400,14281,22031,15975,13038,20750,18707,56489",0.000286437000426347
|
| 153 |
+
"Estrogen signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04915",0.000145703411471315,"268482,14281,20418,224129,15200,21802,16653,66809,18707",0.000312495474602952
|
| 154 |
+
"Sphingolipid metabolism - Mus musculus (house mouse) Homo sapiens mmu00600",0.000150296090340472,"67260,19012,71949,230101,11605,58994",0.000320238728437869
|
| 155 |
+
"NF-kappa B signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04064",0.000161698443779635,"22031,19225,105844,74256,15894,20315,100862177,100504239",0.000342296705663383
|
| 156 |
+
"Apoptosis - Mus musculus (house mouse) Homo sapiens mmu04210",0.000162991854134241,"14281,229445,18211,13038,66593,11461,16653,18707,16188",0.000342808673856532
|
| 157 |
+
"Thyroid cancer - Mus musculus (house mouse) Homo sapiens mmu05216",0.00017799429947637,"12550,20183,12575,18211,16653",0.000371962446341645
|
| 158 |
+
"Endometrial cancer - Mus musculus (house mouse) Homo sapiens mmu05213",0.000182867598316688,"12550,11789,12575,16653,17350,18707",0.000374936082083272
|
| 159 |
+
"Allograft rejection - Mus musculus (house mouse) Homo sapiens mmu05330",0.000182867598316688,"240095,14960,15018,110557,14961,100529082",0.000374936082083272
|
| 160 |
+
"Graft-versus-host disease - Mus musculus (house mouse) Homo sapiens mmu05332",0.000182867598316688,"240095,14960,15018,110557,14961,100529082",0.000374936082083272
|
| 161 |
+
"cGMP-PKG signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04022",0.000208113498346626,"224129,18160,18018,60596,234889,54611,11553,11549,73333,110893",0.00042403125288125
|
| 162 |
+
"TGF-beta signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04350",0.000221566687889175,"12667,66313,15904,12166,110542,12160,21825,15901",0.000445868766986858
|
| 163 |
+
"C-type lectin receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04625",0.000221566687889175,"16653,170786,19225,18018,74256,13654,18707,56489",0.000445868766986858
|
| 164 |
+
"Neutrophil extracellular trap formation - Mus musculus (house mouse) Homo sapiens mmu04613",0.000243231085508763,"15081,11461,18707,14293,14289,232440,319190,319176,73333,319162,14294",0.000486462171017527
|
| 165 |
+
"Taurine and hypotaurine metabolism - Mus musculus (house mouse) Homo sapiens mmu00430",0.000249124977938902,"14417,55990,73748,14415",0.000495211846390744
|
| 166 |
+
"Salivary secretion - Mus musculus (house mouse) Homo sapiens mmu04970",0.000262567395295485,"224129,12182,60596,234889,11549,20192,17105",0.000515644402809206
|
| 167 |
+
"Rheumatoid arthritis - Mus musculus (house mouse) Homo sapiens mmu05323",0.000262567395295485,"14281,66237,13038,14960,15894,20315,14961",0.000515644402809206
|
| 168 |
+
"Mismatch repair - Mus musculus (house mouse) Homo sapiens mmu03430",0.000298157072258942,"68240,17685,17350,18861",0.000582031170996497
|
| 169 |
+
"Thyroid hormone signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04919",0.000354260775498985,"20183,76199,18129,11461,114875,16653,210789,18707",0.000687434600075412
|
| 170 |
+
"Fc epsilon RI signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04664",0.000372574304762309,"26400,16653,18707,329502,78390,211429",0.00071869362930481
|
| 171 |
+
"Pyruvate metabolism - Mus musculus (house mouse) Homo sapiens mmu00620",0.000408255292354325,"107476,109801,11669,100705,110695",0.000782889560632411
|
| 172 |
+
"alpha-Linolenic acid metabolism - Mus musculus (house mouse) Homo sapiens mmu00592",0.000416353063096123,"53357,329502,78390,211429",0.000793749114440562
|
| 173 |
+
"Complement and coagulation cascades - Mus musculus (house mouse) Homo sapiens mmu04610",0.000421912719017294,"19128,12509,20700,20703,20701,12268,20702",0.000799671781393244
|
| 174 |
+
"Adrenergic signaling in cardiomyocytes - Mus musculus (house mouse) Homo sapiens mmu04261",0.000450770939110406,"56808,224129,12322,21956,20272,16526,11549,54376,110893",0.000849429630924812
|
| 175 |
+
"IL-17 signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04657",0.000510305386979089,"14282,14281,22031,16819,19225,56489,20201",0.000956089403190708
|
| 176 |
+
"Glycosphingolipid biosynthesis - lacto and neolacto series - Mus musculus (house mouse) Homo sapiens mmu00601",0.000564641840125298,"56375,231727,72297,14344",0.00105184708503341
|
| 177 |
+
"Huntington disease - Mus musculus (house mouse) Homo sapiens mmu05016",0.000585670284035,"67951,26400,75512,67665,14812,13417,66091,227058,52639,78174,381917,330355,73333",0.0010848210942921
|
| 178 |
+
"Adipocytokine signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04920",0.000595833764078148,"20183,20528,21938,108097,72993,100705",0.00109741133948857
|
| 179 |
+
"Hepatitis C - Mus musculus (house mouse) Homo sapiens mmu05160",0.000646658359833786,"22031,15975,12575,19106,16653,18707,12571,56489,23960",0.00118432935565064
|
| 180 |
+
"Mitophagy - animal - Mus musculus (house mouse) Homo sapiens mmu04137",0.000650427824616891,"66313,75266,50873,59026,170731,16653,72825",0.00118457804930227
|
| 181 |
+
"Prolactin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04917",0.000689612468286362,"12444,14281,20418,16653,14430,18707",0.00124206444564284
|
| 182 |
+
"Autoimmune thyroid disease - Mus musculus (house mouse) Homo sapiens mmu05320",0.000689612468286362,"240095,14960,15018,110557,14961,100529082",0.00124206444564284
|
| 183 |
+
"Gastric acid secretion - Mus musculus (house mouse) Homo sapiens mmu04971",0.000740583796159503,"224129,12322,11461,16526,20606,22350",0.00132654020630768
|
| 184 |
+
"Aldosterone synthesis and secretion - Mus musculus (house mouse) Homo sapiens mmu04925",0.000774259837668402,"224129,15370,12322,18160,223604,12326,231871",0.00137928255234918
|
| 185 |
+
"Chronic myeloid leukemia - Mus musculus (house mouse) Homo sapiens mmu05220",0.000794416517844964,"20418,12575,16653,12402,18707,12571",0.00140749883052966
|
| 186 |
+
"ATP-dependent chromatin remodeling - Mus musculus (house mouse) Homo sapiens mmu03082",0.000812637453723799,"70127,83797,67155,11461,233532,232440,319176,319162",0.00142430005330085
|
| 187 |
+
"Yersinia infection - Mus musculus (house mouse) Homo sapiens mmu05135",0.000812637453723799,"26400,14281,12504,11461,18018,268973,18707,54353",0.00142430005330085
|
| 188 |
+
"JAK-STAT signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04630",0.000870542115603629,"12444,16161,237313,15975,12575,16453,18707,12982,16188",0.00151762957051756
|
| 189 |
+
"Propanoate metabolism - Mus musculus (house mouse) Homo sapiens mmu00640",0.000967393775943395,"13171,107476,73724,100705",0.00167750197317844
|
| 190 |
+
"Toxoplasmosis - Mus musculus (house mouse) Homo sapiens mmu05145",0.00102132794960084,"16775,16782,16780,14960,54396,14961,16145",0.00176165561677182
|
| 191 |
+
"NOD-like receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04621",0.00106521865620613,"22031,15975,170731,56338,268973,56489,23960,195046,54396,637515",0.00182769095749052
|
| 192 |
+
"Linoleic acid metabolism - Mus musculus (house mouse) Homo sapiens mmu00591",0.00114885190567509,"13106,53357,329502,78390,211429",0.00196086765052397
|
| 193 |
+
"Coronavirus disease - Mus musculus (house mouse) Homo sapiens mmu05171",0.00122418028156469,"14281,22031,15975,19106,15200,18707,56489,108169072,27367,23960,12268,22121,433745",0.00207855610307338
|
| 194 |
+
"Valine, leucine and isoleucine degradation - Mus musculus (house mouse) Homo sapiens mmu00280",0.00135067241163518,"13171,56357,11669,73724,110695",0.00226968662986117
|
| 195 |
+
"Regulation of lipolysis in adipocytes - Mus musculus (house mouse) Homo sapiens mmu04923",0.00135067241163518,"224129,18160,19225,18166,18707",0.00226968662986117
|
| 196 |
+
"Circadian rhythm - Mus musculus (house mouse) Homo sapiens mmu04710",0.00137817762617865,"18626,213311,225998,108097",0.0023040302878679
|
| 197 |
+
"Hedgehog signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04340",0.00146084267704258,"12444,56788,66313,16568,68525",0.00242976894242796
|
| 198 |
+
"Arrhythmogenic right ventricular cardiomyopathy - Mus musculus (house mouse) Homo sapiens mmu05412",0.00151451789104487,"56808,11461,11472,54376,110893,213119",0.00250625803289658
|
| 199 |
+
"Leukocyte transendothelial migration - Mus musculus (house mouse) Homo sapiens mmu04670",0.00169857122764814,"11461,21838,171486,15894,18707,22350,20315",0.00278947210743566
|
| 200 |
+
"PD-L1 expression and PD-1 checkpoint pathway in cancer - Mus musculus (house mouse) Homo sapiens mmu05235",0.00170424235695496,"12503,14281,12504,16653,18018,18707",0.00278947210743566
|
| 201 |
+
"Renin-angiotensin system - Mus musculus (house mouse) Homo sapiens mmu04614",0.00171133258124887,"240028,16790,13646,16617",0.00278947210743566
|
| 202 |
+
"Inflammatory bowel disease - Mus musculus (house mouse) Homo sapiens mmu05321",0.00196849402340238,"16161,16182,18018,14960,14961",0.00319268184890138
|
| 203 |
+
"Aldosterone-regulated sodium reabsorption - Mus musculus (house mouse) Homo sapiens mmu04960",0.00209656106523012,"20393,16000,16653,18707",0.00338355894685653
|
| 204 |
+
"Basal cell carcinoma - Mus musculus (house mouse) Homo sapiens mmu05217",0.00211328458441964,"11789,14365,14368,12575,93897",0.00339374765773795
|
| 205 |
+
"Progesterone-mediated oocyte maturation - Mus musculus (house mouse) Homo sapiens mmu04914",0.00225733147326025,"16001,16000,224129,268930,16653,18707",0.0036029898304789
|
| 206 |
+
"Lysine degradation - Mus musculus (house mouse) Homo sapiens mmu00310",0.00226568378910483,"214162,209692,64707,11669,110695",0.0036029898304789
|
| 207 |
+
"Long-term potentiation - Mus musculus (house mouse) Homo sapiens mmu04720",0.00277083614151071,"12322,14812,16653,12326,14811",0.00438491544724511
|
| 208 |
+
"Relaxin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04926",0.00292230482010871,"26400,14281,20418,224129,16653,18707,14708",0.00460227715630647
|
| 209 |
+
"Autophagy - animal - Mus musculus (house mouse) Homo sapiens mmu04140",0.00297397708545308,"27103,16001,52187,16653,100502841,18707,52639,72145",0.00466113716277742
|
| 210 |
+
"Homologous recombination - Mus musculus (house mouse) Homo sapiens mmu03440",0.00303879718210365,"21975,114714,68240,12189",0.00473994201610426
|
| 211 |
+
"Central carbon metabolism in cancer - Mus musculus (house mouse) Homo sapiens mmu05230",0.00314987512985928,"216019,18211,16653,18707,20539",0.00488980615397202
|
| 212 |
+
"Pantothenate and CoA biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00770",0.0032120707437745,"11669,103149,73748",0.00496272541455207
|
| 213 |
+
"Melanogenesis - Mus musculus (house mouse) Homo sapiens mmu04916",0.00324596457621063,"14365,14368,224129,12322,16653,93897",0.00499143609360691
|
| 214 |
+
"Nicotinate and nicotinamide metabolism - Mus musculus (house mouse) Homo sapiens mmu00760",0.00331291390115332,"12182,75387,225994,68352",0.00504677538213076
|
| 215 |
+
"Intestinal immune network for IgA production - Mus musculus (house mouse) Homo sapiens mmu04672",0.00331291390115332,"20300,14960,20315,14961",0.00504677538213076
|
| 216 |
+
"Glutathione metabolism - Mus musculus (house mouse) Homo sapiens mmu00480",0.00401771151420727,"75512,18263,14768,16790,14867",0.00609197187735614
|
| 217 |
+
"Thyroid hormone synthesis - Mus musculus (house mouse) Homo sapiens mmu04918",0.00425887811173777,"114479,75512,70337,11889,224129",0.00642775122419682
|
| 218 |
+
"Pancreatic cancer - Mus musculus (house mouse) Homo sapiens mmu05212",0.00477185867467182,"12575,21802,16653,18707,12571",0.0071687830780784
|
| 219 |
+
"Bacterial invasion of epithelial cells - Mus musculus (house mouse) Homo sapiens mmu05100",0.00504412539706173,"12550,20418,11461,12402,18707",0.00754304990569782
|
| 220 |
+
"Histidine metabolism - Mus musculus (house mouse) Homo sapiens mmu00340",0.00595461549127695,"11669,109731,110695",0.00886394817422961
|
| 221 |
+
"Prion disease - Mus musculus (house mouse) Homo sapiens mmu05020",0.00649188784987015,"67951,17968,14812,66091,13653,18707,78174,20192,14811,73333",0.00961979745026213
|
| 222 |
+
"Fatty acid degradation - Mus musculus (house mouse) Homo sapiens mmu00071",0.00656822270473466,"13177,11363,11669,110695",0.00968887150110181
|
| 223 |
+
"Phototransduction - Mus musculus (house mouse) Homo sapiens mmu04744",0.0066283621976709,"19739,19674,225600",0.00973354088486808
|
| 224 |
+
"Insulin secretion - Mus musculus (house mouse) Homo sapiens mmu04911",0.00800773392688975,"224129,14652,11516,12322,12424",0.0117063733639734
|
| 225 |
+
"Virion - Human immunodeficiency virus - Mus musculus (house mouse) Homo sapiens mmu03260",0.0085396062920342,"12504,170786",0.0124281770142998
|
| 226 |
+
"Cardiac muscle contraction - Mus musculus (house mouse) Homo sapiens mmu04260",0.00921765308758486,"56808,21956,78174,54376,110893",0.0133553551402341
|
| 227 |
+
"ABC transporters - Mus musculus (house mouse) Homo sapiens mmu02010",0.00962472381753213,"11303,27421,224814,381072",0.0138834511704224
|
| 228 |
+
"Galactose metabolism - Mus musculus (house mouse) Homo sapiens mmu00052",0.0106614295261939,"216019,11605,14430",0.0152439737962246
|
| 229 |
+
"Mucin type O-glycan biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00512",0.0106614295261939,"72297,231050,271786",0.0152439737962246
|
| 230 |
+
"Phosphatidylinositol signaling system - Mus musculus (house mouse) Homo sapiens mmu04070",0.012517667395432,"228550,114875,27399,320127,18707",0.0178199107900036
|
| 231 |
+
"Biosynthesis of unsaturated fatty acids - Mus musculus (house mouse) Homo sapiens mmu01040",0.0125942356805834,"20249,329065,30963",0.017850960138566
|
| 232 |
+
"GnRH secretion - Mus musculus (house mouse) Homo sapiens mmu04929",0.01277942255874,"20750,16653,18707,22067",0.0180350292387413
|
| 233 |
+
"Diabetic cardiomyopathy - Mus musculus (house mouse) Homo sapiens mmu05415",0.0132550069101062,"20528,27273,12322,210789,66091,18707,78174,73333",0.0186255700547182
|
| 234 |
+
"Virion - Flavivirus and Alphavirus - Mus musculus (house mouse) Homo sapiens mmu03264",0.0143872294214307,"22174,170786",0.0201297716368516
|
| 235 |
+
"Primary immunodeficiency - Mus musculus (house mouse) Homo sapiens mmu05340",0.0147142914948699,"12504,16453,19727",0.020499397552682
|
| 236 |
+
"AGE-RAGE signaling pathway in diabetic complications - Mus musculus (house mouse) Homo sapiens mmu04933",0.0153115948998531,"16653,18018,15894,13653,18707",0.0212407656908601
|
| 237 |
+
"Cornified envelope formation - Mus musculus (house mouse) Homo sapiens mmu04382",0.0153916073129754,"268482,16782,16780,230101,11686,14027,66809,20201",0.0212612880679236
|
| 238 |
+
"Tuberculosis - Mus musculus (house mouse) Homo sapiens mmu05152",0.0156053764391674,"16149,12322,14130,170786,19727,14960,14961",0.0214656232876311
|
| 239 |
+
"Spinocerebellar ataxia - Mus musculus (house mouse) Homo sapiens mmu05017",0.0163834053770796,"69597,14812,18707,52639,14811,73333",0.022441135096336
|
| 240 |
+
"Glucagon signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04922",0.0171730061999729,"107476,12322,235344,108097,100705",0.0234242678710927
|
| 241 |
+
"Acute myeloid leukemia - Mus musculus (house mouse) Homo sapiens mmu05221",0.0181975374287284,"67603,16653,13685,18707",0.0244832881209463
|
| 242 |
+
"Leishmaniasis - Mus musculus (house mouse) Homo sapiens mmu05140",0.0181975374287284,"14281,19225,14960,14961",0.0244832881209463
|
| 243 |
+
"Alanine, aspartate and glutamate metabolism - Mus musculus (house mouse) Homo sapiens mmu00250",0.0182498129245091,"53320,14417,14415",0.0244832881209463
|
| 244 |
+
"Amino sugar and nucleotide sugar metabolism - Mus musculus (house mouse) Homo sapiens mmu00520",0.0182498129245091,"216019,69080,14430",0.0244832881209463
|
| 245 |
+
"Amoebiasis - Mus musculus (house mouse) Homo sapiens mmu05146",0.0191783805314038,"16775,14680,16782,16780,18707",0.0256235739886789
|
| 246 |
+
"Glycine, serine and threonine metabolism - Mus musculus (house mouse) Homo sapiens mmu00260",0.01952376221915,"11656,109731,110695",0.0259785570752771
|
| 247 |
+
"Ferroptosis - Mus musculus (house mouse) Homo sapiens mmu04216",0.0208455930769211,"17254,53945,26570",0.0276246477360825
|
| 248 |
+
"Insulin resistance - Mus musculus (house mouse) Homo sapiens mmu04931",0.0213315983675432,"20528,210789,108097,18707,100705",0.0281542553352999
|
| 249 |
+
"Fat digestion and absorption - Mus musculus (house mouse) Homo sapiens mmu04975",0.0236330290602521,"11303,19012,67800",0.0310659978775894
|
| 250 |
+
"Glycosphingolipid biosynthesis - globo and isoglobo series - Mus musculus (house mouse) Homo sapiens mmu00603",0.0241566009272045,"11605,14344",0.0316267144669425
|
| 251 |
+
"Inositol phosphate metabolism - Mus musculus (house mouse) Homo sapiens mmu00562",0.0248541882738288,"228550,114875,27399,18707",0.0324098615090727
|
| 252 |
+
"Vasopressin-regulated water reabsorption - Mus musculus (house mouse) Homo sapiens mmu04962",0.0250986131552437,"67665,13427,14570",0.0325981987594002
|
| 253 |
+
"Other types of O-glycan biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00514",0.0266120393743797,"224143,231050,271786",0.0344266858573324
|
| 254 |
+
"Other glycan degradation - Mus musculus (house mouse) Homo sapiens mmu00511",0.0269218401804805,"230101,11593",0.0346898019716863
|
| 255 |
+
"Nucleocytoplasmic transport - Mus musculus (house mouse) Homo sapiens mmu03013",0.0278224143973805,"19826,60365,245610,408191,408192",0.0357090830454568
|
| 256 |
+
"Fatty acid biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00061",0.0298078709333924,"107476,100705",0.0378699089334995
|
| 257 |
+
"Lipoic acid metabolism - Mus musculus (house mouse) Homo sapiens mmu00785",0.0298078709333924,"13171,209692",0.0378699089334995
|
| 258 |
+
"Non-alcoholic fatty liver disease - Mus musculus (house mouse) Homo sapiens mmu04932",0.0298544987604582,"14281,13106,66091,108097,18707,78174",0.0378699089334995
|
| 259 |
+
"Cytosolic DNA-sensing pathway - Mus musculus (house mouse) Homo sapiens mmu04623",0.0303980934801686,"70408,54722,70796,56489",0.0384099940873448
|
| 260 |
+
"Type II diabetes mellitus - Mus musculus (house mouse) Homo sapiens mmu04930",0.0314383182249157,"20528,216019,18707",0.0395710105842568
|
| 261 |
+
"RNA degradation - Mus musculus (house mouse) Homo sapiens mmu03018",0.0315872301062652,"12227,12228,231464,22057",0.0396055269793941
|
| 262 |
+
"Glycosaminoglycan degradation - Mus musculus (house mouse) Homo sapiens mmu00531",0.0359263149284303,"15932,545291",0.0448734814814876
|
| 263 |
+
"Peroxisome - Mus musculus (house mouse) Homo sapiens mmu04146",0.0366139087911143,"12359,19301,67528,26378",0.0455577643736766
|
| 264 |
+
"Polycomb repressive complex - Mus musculus (house mouse) Homo sapiens mmu03083",0.0379383213111521,"212391,52609,50496,353282",0.0470262081651544
|
| 265 |
+
"PPAR signaling pathway - Mus musculus (house mouse) Homo sapiens mmu03320",0.0392898821687318,"20183,11363,20249,329065",0.0485170514659339
|
| 266 |
+
"Taste transduction - Mus musculus (house mouse) Homo sapiens mmu04742",0.0435075057870138,"18575,14399,18574,15552",0.053522441081383
|
| 267 |
+
"Pyrimidine metabolism - Mus musculus (house mouse) Homo sapiens mmu00240",0.0484444033673713,"22271,54369,103149",0.0593717123976054
|
| 268 |
+
"Asthma - Mus musculus (house mouse) Homo sapiens mmu05310",0.0494417443857017,"14960,14961",0.0603670736694336
|
| 269 |
+
"Butanoate metabolism - Mus musculus (house mouse) Homo sapiens mmu00650",0.0567806565612424,"14417,14415",0.0680532869079597
|
| 270 |
+
"Hippo signaling pathway - multiple species - Mus musculus (house mouse) Homo sapiens mmu04392",0.0567806565612424,"56289,215653",0.0680532869079597
|
| 271 |
+
"Folate transport and metabolism - Mus musculus (house mouse) Homo sapiens mmu04981",0.0567806565612424,"53320,101488",0.0680532869079597
|
| 272 |
+
"Collecting duct acid secretion - Mus musculus (house mouse) Homo sapiens mmu04966",0.0567806565612424,"20533,66237",0.0680532869079597
|
| 273 |
+
"Maturity onset diabetes of the young - Mus musculus (house mouse) Homo sapiens mmu04950",0.0567806565612424,"21410,21405",0.0680532869079597
|
| 274 |
+
"Endocrine and other factor-regulated calcium reabsorption - Mus musculus (house mouse) Homo sapiens mmu04961",0.0571781158255804,"13646,16617,110893",0.0682786291543561
|
| 275 |
+
"Chagas disease - Mus musculus (house mouse) Homo sapiens mmu05142",0.0610519329903192,"12503,14281,14680,18707",0.0726384312220587
|
| 276 |
+
"Notch signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04330",0.0641812508653678,"19164,18129,15208",0.0760839555713088
|
| 277 |
+
"Fatty acid elongation - Mus musculus (house mouse) Homo sapiens mmu00062",0.068438877249005,"75778,30963",0.0805453934410673
|
| 278 |
+
"Glycosylphosphatidylinositol (GPI)-anchor biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00563",0.068438877249005,"18701,225651",0.0805453934410673
|
| 279 |
+
"Neomycin, kanamycin and gentamicin biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00524",0.0695596678420736,"216019",0.0815699702032949
|
| 280 |
+
"Ribosome biogenesis in eukaryotes - Mus musculus (house mouse) Homo sapiens mmu03008",0.0699181383981639,"73674,66161,213773,245610,100019",0.0816964627878188
|
| 281 |
+
"Glycolysis / Gluconeogenesis - Mus musculus (house mouse) Homo sapiens mmu00010",0.0715586224791162,"216019,11669,110695",0.0833146818863996
|
| 282 |
+
"RNA polymerase - Mus musculus (house mouse) Homo sapiens mmu03020",0.076606990380589,"20017,70408",0.088875013751146
|
| 283 |
+
"Glyoxylate and dicarboxylate metabolism - Mus musculus (house mouse) Homo sapiens mmu00630",0.0808006940503487,"12359,73724",0.0934078945404741
|
| 284 |
+
"Phosphonate and phosphinate metabolism - Mus musculus (house mouse) Homo sapiens mmu00440",0.0828802106868017,"28042",0.095473316904231
|
| 285 |
+
"Cortisol synthesis and secretion - Mus musculus (house mouse) Homo sapiens mmu04927",0.0846485700973768,"224129,15370,16526",0.0971670206047354
|
| 286 |
+
"RIG-I-like receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04622",0.0873808655139507,"22031,74256,56489",0.0999514461668349
|
| 287 |
+
"Tight junction - Mus musculus (house mouse) Homo sapiens mmu04530",0.096708343789317,"26400,102098,11461,108097,22350",0.110233986277333
|
| 288 |
+
"Fructose and mannose metabolism - Mus musculus (house mouse) Homo sapiens mmu00051",0.0982394640526499,"216019,69080",0.111589077634717
|
| 289 |
+
"Ribosome - Mus musculus (house mouse) Homo sapiens mmu03010",0.101737449620311,"78523,67212,121022,232536,108169072,27367,22121,433745",0.115161140889658
|
| 290 |
+
"Riboflavin metabolism - Mus musculus (house mouse) Homo sapiens mmu00740",0.108952266338487,"11431",0.122901172409504
|
| 291 |
+
"Tyrosine metabolism - Mus musculus (house mouse) Homo sapiens mmu00350",0.111939916657735,"14085,109731",0.125835906311799
|
| 292 |
+
"Sphingolipid signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04071",0.119630070651305,"67260,71949,16653,18707",0.134018567121393
|
| 293 |
+
"Base excision repair - Mus musculus (house mouse) Homo sapiens mmu03410",0.145574881270385,"21665,545124",0.162525381144334
|
| 294 |
+
"Carbohydrate digestion and absorption - Mus musculus (house mouse) Homo sapiens mmu04973",0.155532890498634,"216019,18707",0.173050246766398
|
| 295 |
+
"Cholesterol metabolism - Mus musculus (house mouse) Homo sapiens mmu04979",0.165615461244665,"11303,16891",0.183641633897146
|
| 296 |
+
"Non-homologous end-joining - Mus musculus (house mouse) Homo sapiens mmu03450",0.170937541832337,"19090",0.188900469957091
|
| 297 |
+
"Glycosaminoglycan biosynthesis - keratan sulfate - Mus musculus (house mouse) Homo sapiens mmu00533",0.182807565890172,"56375",0.201335359730392
|
| 298 |
+
"Mineral absorption - Mus musculus (house mouse) Homo sapiens mmu04978",0.186094584417396,"53945,110893",0.204265436094515
|
| 299 |
+
"mRNA surveillance pathway - Mus musculus (house mouse) Homo sapiens mmu03015",0.187364781691476,"19826,60365,245610",0.204969526279937
|
| 300 |
+
"Thiamine metabolism - Mus musculus (house mouse) Homo sapiens mmu00730",0.194507746232425,"11431",0.212071990875487
|
| 301 |
+
"Selenocompound metabolism - Mus musculus (house mouse) Homo sapiens mmu00450",0.217408256014336,"21743",0.236250304868912
|
| 302 |
+
"Pancreatic secretion - Mus musculus (house mouse) Homo sapiens mmu04972",0.227952223412653,"224129,12182,12424",0.24596682710023
|
| 303 |
+
"Primary bile acid biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00120",0.22861333929868,"12642",0.24596682710023
|
| 304 |
+
"Natural killer cell mediated cytotoxicity - Mus musculus (house mouse) Homo sapiens mmu04650",0.22861333929868,"12503",0.24596682710023
|
| 305 |
+
"Arginine biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00220",0.261275717522459,"18416",0.277445875935901
|
| 306 |
+
"Phenylalanine metabolism - Mus musculus (house mouse) Homo sapiens mmu00360",0.261275717522459,"109731",0.277445875935901
|
| 307 |
+
"Biosynthesis of various nucleotide sugars - Mus musculus (house mouse) Homo sapiens mmu00541",0.261275717522459,"69080",0.277445875935901
|
| 308 |
+
"Virion - Lassa virus and SFTS virus - Mus musculus (house mouse) Homo sapiens mmu03273",0.261275717522459,"170786",0.277445875935901
|
| 309 |
+
"Pertussis - Mus musculus (house mouse) Homo sapiens mmu05133",0.302093763789309,"14281,12268",0.319748594140633
|
| 310 |
+
"Vitamin digestion and absorption - Mus musculus (house mouse) Homo sapiens mmu04977",0.312670472856016,"53320",0.329872408255862
|
| 311 |
+
"Oxidative phosphorylation - Mus musculus (house mouse) Homo sapiens mmu00190",0.328368703531495,"66237,66091,78174",0.34531676564925
|
| 312 |
+
"Autophagy - other - Mus musculus (house mouse) Homo sapiens mmu04136",0.369649215304488,"52639",0.386236039068151
|
| 313 |
+
"Apoptosis - multiple species - Mus musculus (house mouse) Homo sapiens mmu04215",0.369649215304488,"66593",0.386236039068151
|
| 314 |
+
"Pentose phosphate pathway - Mus musculus (house mouse) Homo sapiens mmu00030",0.387573068984444,"71336",0.402384778627161
|
| 315 |
+
"SNARE interactions in vesicular transport - Mus musculus (house mouse) Homo sapiens mmu04130",0.387573068984444,"53611",0.402384778627161
|
| 316 |
+
"Starch and sucrose metabolism - Mus musculus (house mouse) Homo sapiens mmu00500",0.396343075027413,"216019",0.410183626853767
|
| 317 |
+
"DNA replication - Mus musculus (house mouse) Homo sapiens mmu03030",0.404987570865291,"68240",0.417803633234446
|
| 318 |
+
"One carbon pool by folate - Mus musculus (house mouse) Homo sapiens mmu00670",0.413508351610087,"110695",0.425248336356115
|
| 319 |
+
"Protein processing in endoplasmic reticulum - Mus musculus (house mouse) Homo sapiens mmu04141",0.476903457680544,"26400,50873,66326",0.488901028942947
|
| 320 |
+
"Virion - Hepatitis viruses - Mus musculus (house mouse) Homo sapiens mmu03272",0.520755596701581,"15530",0.532182835500675
|
| 321 |
+
"Cysteine and methionine metabolism - Mus musculus (house mouse) Homo sapiens mmu00270",0.560492883410785,"100041585",0.569223302155502
|
| 322 |
+
"N-Glycan biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00510",0.560492883410785,"17309",0.569223302155502
|
| 323 |
+
"Nucleotide excision repair - Mus musculus (house mouse) Homo sapiens mmu03420",0.56678795312173,"68240",0.573828797259888
|
| 324 |
+
"Legionellosis - Mus musculus (house mouse) Homo sapiens mmu05134",0.572992913720444,"268973",0.578314829327755
|
| 325 |
+
"Spliceosome - Mus musculus (house mouse) Homo sapiens mmu03040",0.824215051765366,"67439,20624,27366,66810,101214,60321,64340,60365,115487843,115486569,115487345,115489188",0.829302798998485
|
| 326 |
+
"Olfactory transduction - Mus musculus (house mouse) Homo sapiens mmu04740",0.828879702177402,"18575,12789,18574,14680,12322,258837,14708,56860,629524,258463,18330,545140,110893,634104",0.831430101261025
|
| 327 |
+
"Aminoacyl-tRNA biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00970",0.998701482189689,"71941",0.998701482189689
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/kegg_5xfad.csv
ADDED
|
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|
|
|
| 1 |
+
"pathway","pvalue","overlap_genes","padj"
|
| 2 |
+
"Epstein-Barr virus infection - Mus musculus (house mouse) Homo sapiens mmu05169",1.96764693618455e-62,"11651,12502,16391,20848,11652,12505,14991,15182,26420,53859,26419,17869,15976,18037,19106,21356,15001,21355,21926,14102,18034,12566,54123,12370,20846,22352,24088,18033,18710,23961,12229,16453,71609,12501,12500,17874,246727,246728,26398,234779,15945,100038882,15015,14960,21354,15894,228607,14998,213233,20847,12571,230073,15002,17096,12495,246730,19094,15039,266632,15018,14969,12010,17060,14972,23960,15040,15007,110557,14964,14961,14999",6.70967605238931e-60
|
| 3 |
+
"Herpes simplex virus 1 infection - Mus musculus (house mouse) Homo sapiens mmu05168",3.54655633796264e-61,"16402,11651,16391,11652,20815,14991,15979,15980,15976,19106,12266,21356,15001,21355,72512,21926,16149,14102,54123,12370,20846,20684,71586,332579,24088,18033,18710,57317,23961,78781,21937,13685,71609,11796,214763,17874,246727,246728,20304,20293,20296,15015,14960,21354,228607,14998,213233,20847,230073,15002,231805,69550,246730,12702,15039,266632,15018,14969,12010,14972,545812,23960,15040,15007,110557,14964,14961,14999",6.04687855622631e-59
|
| 4 |
+
"Osteoclast differentiation - Mus musculus (house mouse) Homo sapiens mmu04380",6.8846744828262e-60,"11651,20375,16391,16822,14282,11652,26395,13057,21812,14200,12977,14129,17969,15979,26420,53859,14281,26419,19057,15980,15976,83433,21926,12978,18034,16177,20846,21934,17970,14130,16175,19055,18033,18710,14284,21682,21937,22177,11937,12229,21813,18018,19058,234779,12703,20847,12702,19094,18733,246256,14131,17060,14728,26413,232801,17972,14727",7.82557999547912e-58
|
| 5 |
+
"Tuberculosis - Mus musculus (house mouse) Homo sapiens mmu05152",4.2149792385833e-52,"16414,11651,27060,11652,13033,14129,16803,16784,16985,15979,26420,17534,12325,26419,19057,15980,16155,18044,12266,15001,21926,16149,12370,20846,14130,332579,16175,24088,19055,18033,242341,21937,16409,16411,71609,16154,17874,19058,14960,14998,13040,21898,192656,15002,21897,12475,21899,19094,12611,14127,246256,14131,266632,14969,26413,14961,56644,14999",3.59326980089227e-50
|
| 6 |
+
"Human T-cell leukemia virus 1 infection - Mus musculus (house mouse) Homo sapiens mmu05166",7.12803658722876e-51,"16414,11651,12502,20375,11652,26395,107995,21812,14991,26420,22333,53859,14281,210044,26419,19057,17869,13383,15001,21926,18034,12566,16177,19055,18033,21894,18710,50883,16653,17000,21937,16186,11513,16453,12501,12500,12442,21813,18018,26398,19058,15015,14960,15894,14998,13654,13653,15002,12257,22695,15039,110196,15018,14969,12010,14972,26413,15040,15007,16185,110557,14964,14961,14999",4.86132095249001e-49
|
| 7 |
+
"Cytokine-cytokine receptor interaction - Mus musculus (house mouse) Homo sapiens mmu04060",3.85054627206932e-50,"20302,16170,19116,50931,21812,57916,12977,16164,66102,20305,20303,20308,15979,14560,18414,21935,15980,16155,15976,55985,21926,12978,14102,77125,16174,17082,16177,21934,16963,269275,11477,16181,54450,16175,16194,21949,21938,12986,20311,17329,17000,21937,60504,16190,16186,24099,76527,16154,21813,57914,15945,20304,20293,20296,21950,80901,12766,13051,18413,12982,16185,16188,107527,12983,12984,100504346,12774,12803",1.96268507384696e-48
|
| 8 |
+
"Human immunodeficiency virus 1 infection - Mus musculus (house mouse) Homo sapiens mmu05170",4.02897229235446e-50,"11651,12502,11652,26395,80287,14991,12534,26420,14281,26419,19057,14083,21356,21355,72512,21926,14102,12370,24088,19055,18033,21938,18710,14688,16653,21937,18479,99375,71609,12501,12500,12442,214763,17874,14678,18018,19354,19058,234779,14672,15015,21354,213233,14710,21898,69550,19094,15039,319236,209387,14677,266632,667823,15018,12010,14972,26413,15040,15007,14707,110557,14964,12774",1.96268507384696e-48
|
| 9 |
+
"Influenza A - Mus musculus (house mouse) Homo sapiens mmu05164",5.87578420906745e-49,"217069,17857,11651,16391,11652,26395,15979,22333,58185,15980,15976,17858,19106,15001,21926,14102,77125,54123,12370,20846,71586,16175,18033,18710,23961,21937,66824,71609,17874,246727,246728,216799,15945,20304,20293,20296,14960,15894,228607,14998,21898,20847,12571,230073,15002,170743,246730,12702,110196,266632,14969,26413,23960,14961,14999",2.504553019115e-47
|
| 10 |
+
"Chagas disease - Mus musculus (house mouse) Homo sapiens mmu05142",7.31616594102413e-48,"20302,11651,12502,11652,51792,21812,15979,26420,12062,14281,26419,15980,12266,21926,72930,14675,14102,12370,12633,24088,18033,18710,269643,21937,12501,12500,21813,17874,14678,26398,14672,14676,20304,20293,20296,12259,12262,12260,21898,18796,21899,19094,14677,266632,26413",2.77201398432136e-46
|
| 11 |
+
"NOD-like receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04621",1.68291048043916e-47,"16391,13057,215999,13058,26420,22333,15519,59079,26419,13030,18753,56532,69146,15976,72512,21926,54123,12364,12370,20846,332579,18033,55932,14469,71914,18439,23961,66824,11796,17874,246727,246728,216799,12363,106512,20304,20293,20296,228607,383619,107607,21898,20847,18796,229900,192656,15944,246730,19094,266632,26413,23960,54396,17951,15951,17952,17948,229898",5.73872473829755e-46
|
| 12 |
+
"Lysosome biogenesis - Mus musculus (house mouse) Homo sapiens mmu04142",2.27035771882246e-47,"14667,27060,27419,13423,13034,17159,13033,11974,64138,16784,19025,12514,66848,53599,71279,74008,19141,67963,13039,15212,13030,211286,97998,17939,56722,27426,63959,65221,16889,13041,15211,12512,110006,18173,26889,14466,74245,242341,16792,71665,100561,12492,71720,13032,12752,12751,11593,64933,11886,192654,69091,13036,15932,75612,109685,52120,13040,64291,170743,12091,233979,22320",7.03810892834963e-46
|
| 13 |
+
"Kaposi sarcoma-associated herpesvirus infection - Mus musculus (house mouse) Homo sapiens mmu05167",5.2959711178454e-45,"11651,16391,15162,20848,11652,26395,14991,15979,26420,30955,320207,15251,14281,26419,19057,17869,12524,15976,19106,12266,14102,21416,54123,12370,20846,19055,18033,18710,14688,16653,21937,11601,71609,18018,26398,19058,234779,15015,14173,15894,14710,20847,12571,17096,22695,19094,15039,15018,14972,239849,26413,15040,15007,14707,110557,14964,12774",1.45189045679669e-43
|
| 14 |
+
"Human cytomegalovirus infection - Mus musculus (house mouse) Homo sapiens mmu05163",5.53506625758267e-45,"14673,20302,11651,20848,11652,26395,14991,20303,210044,19057,17869,14083,16155,21356,21355,72512,21926,14102,12370,16177,16194,19055,18033,18710,14688,16653,21937,13685,11513,71609,16154,214763,14678,18018,19354,19058,14672,20304,20293,20296,15015,21354,213233,14710,19219,18796,12571,19094,15039,14677,15018,12010,14972,26413,15040,15007,14707,110557,14964,12774",1.45189045679669e-43
|
| 15 |
+
"Chemokine signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04062",1.71168692268448e-43,"20302,11651,15162,20848,11652,26395,17969,66102,20305,20303,20308,94176,30955,320207,210044,18753,14083,55985,20846,16963,18033,18710,14191,18762,14688,20311,17329,16653,18479,22376,11513,16453,14678,19354,22324,234779,15945,20304,20293,20296,14710,20847,18796,17096,20416,80901,12766,13051,14677,26413,14707,100504346,12774",4.1691802902529e-42
|
| 16 |
+
"Phagosome - Mus musculus (house mouse) Homo sapiens mmu04145",1.17501557440888e-42,"16414,16402,27060,13057,13058,11974,14129,17969,14991,16784,17534,13039,16419,12266,15001,21355,57743,17970,14130,24088,21827,242341,13426,108078,16409,15015,14960,21354,14998,13040,21898,21825,15002,22146,12475,21899,226421,15039,246256,14131,15018,14969,14972,15040,15007,17972,110557,14964,14961,56644,14999",2.67120207248953e-41
|
| 17 |
+
"MAPK signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04010",1.10147903523608e-41,"14673,11651,12297,20111,11652,26395,21812,12977,18099,12298,16000,26420,53859,14281,26419,19057,11600,17869,19252,21926,12978,14102,18034,16177,12292,16175,13638,19055,18033,11876,17346,16653,21937,18479,110651,11601,319520,71609,71785,21813,17874,102626,18018,19354,26398,19058,240672,14164,14173,26411,18218,12293,12064,12475,19094,235584,18783,266632,19043,26413,240168",2.34752719384691e-40
|
| 18 |
+
"Human papillomavirus infection - Mus musculus (house mouse) Homo sapiens mmu05165",4.29326397489135e-41,"17857,16402,12833,11651,27060,16391,11652,26395,51792,11974,14991,17305,16362,15182,14083,13383,16419,15976,17858,19106,21926,72930,93687,14102,21416,12566,12370,20846,22409,12841,19650,21827,18033,242341,18710,18762,269643,20750,23962,16653,21937,13685,71609,270118,100038882,15015,18759,12643,19219,20847,21825,12571,231655,103768,101206,15039,15018,14972,26413,12829,15040,15007,110557,14964,12828",8.61178244375264e-40
|
| 19 |
+
"Th17 cell differentiation - Mus musculus (house mouse) Homo sapiens mmu04659",8.85246286243975e-40,"12502,20848,50931,21812,14462,15979,26420,15251,14281,15519,26419,19057,12394,15980,18037,15001,16177,20846,16194,19055,18033,16797,60504,16190,16186,16453,12501,12500,21813,18018,19058,14960,14998,15002,19094,14969,26413,16185,14961,14999",1.67704990893998e-38
|
| 20 |
+
"Lipid and atherosclerosis - Mus musculus (house mouse) Homo sapiens mmu05417",1.61144126163139e-39,"20302,11651,20848,11652,13057,20656,11303,13058,18024,17969,16803,26420,14281,15519,12325,26419,19057,14083,21926,14102,54123,12370,17970,24088,12368,19055,18033,18710,108078,16653,21937,66824,17874,216799,18018,26398,19058,22324,20304,20293,20296,15894,21898,18796,17096,12475,21899,19094,225471,266632,26413,17972",2.89211300113844e-38
|
| 21 |
+
"Salmonella infection - Mus musculus (house mouse) Homo sapiens mmu05132",1.76782336830108e-39,"11651,19158,74764,11652,26395,56044,72318,66713,26420,30955,14281,15519,16593,26419,56532,17869,105855,69146,67268,21926,21416,12370,19264,50884,24088,18033,74734,11867,13426,21937,18479,66824,71609,11796,12306,17874,216799,26398,12363,226977,107607,21898,192656,22146,80837,12475,21899,226421,19094,266632,26413,17951,56212,17952,17948",3.01413884295334e-38
|
| 22 |
+
"Pathways in cancer - Mus musculus (house mouse) Homo sapiens mmu05200",4.16167044625026e-39,"14673,11651,20375,20848,11652,26395,15368,21812,56044,18024,16164,15182,15979,16000,26420,12062,15251,14281,15519,210044,12325,26419,17869,14083,12394,15980,15976,17685,12978,14102,21416,18034,12566,12370,20846,22409,16194,18033,18710,12986,14688,16653,16190,16186,11513,16453,11606,11796,21813,14678,19354,67168,234779,14672,12606,14164,14173,14710,19219,20847,18796,12571,14677,12982,216033,26413,12829,14296,381810,16185,14707,16188,240168,12983,12984,12828",6.7577601055778e-38
|
| 23 |
+
"PI3K-Akt signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04151",3.28189956137272e-38,"16402,12833,11651,11652,26395,19116,51792,12977,16000,30955,320207,15519,18414,22631,11600,17869,14083,16419,15976,72930,12978,83490,12566,263803,12841,16194,24088,13638,21827,18033,108079,11876,18710,12986,14688,269643,20750,16653,16190,16186,11601,13685,16453,71785,67168,68401,14164,14173,14710,21898,12643,21825,12571,243764,12064,18413,26413,12829,381810,16185,14707,16188,12828",5.08694432012772e-37
|
| 24 |
+
"Measles - Mus musculus (house mouse) Homo sapiens mmu05162",1.09118794020101e-37,"17857,11651,12502,16391,20848,11652,26420,14281,26419,15976,17858,19106,14102,12566,54123,12370,20846,14130,71586,16175,24088,18033,18710,23961,17698,16186,16453,71609,12501,12500,17874,246727,246728,228607,21898,20847,12571,230073,170743,246730,266632,23960,16185",1.61780472873281e-36
|
| 25 |
+
"Toxoplasmosis - Mus musculus (house mouse) Homo sapiens mmu05145",3.91840988740042e-36,"11651,20848,11652,15979,26420,30955,320207,26419,15980,16155,15001,21926,11689,12370,20846,24088,18033,21937,11796,16154,17874,14678,14960,14998,12703,21898,15002,15944,19094,14677,266632,14969,26413,54396,14961,16145,12774,14999",5.56740738168143e-35
|
| 26 |
+
"Leishmaniasis - Mus musculus (house mouse) Homo sapiens mmu05140",3.00554992438239e-35,"16414,15170,13057,13058,14129,17969,15979,14281,15980,12266,15001,21926,20846,17970,16175,24088,18033,16409,17874,14960,14998,21898,15002,19094,246256,14131,266632,14969,26413,17972,14961,14999",4.09957009685758e-34
|
| 27 |
+
"Hepatitis C - Mus musculus (house mouse) Homo sapiens mmu05160",9.91904387380877e-35,"17857,11651,16391,20848,11652,26395,51792,58185,22631,17869,15976,17858,19106,21926,72930,14102,12566,54123,12370,12633,20846,18033,18710,269643,23961,16653,21937,71609,246727,246728,15957,15945,228607,18417,12520,20847,12571,230073,56173,246730,12702,26413,23960",1.30092075421877e-33
|
| 28 |
+
"Toll-like receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04620",3.52428182733246e-34,"20302,11651,16391,11652,26395,16803,20303,26420,14281,26419,12524,15976,21926,54123,12370,20846,24088,18033,18710,20750,17329,27056,17874,26398,15945,20304,21898,20847,170743,21897,12475,21899,19094,225471,266632,26413",4.45103741896432e-33
|
| 29 |
+
"Hematopoietic cell lineage - Mus musculus (house mouse) Homo sapiens mmu04640",2.62233343434477e-33,"16402,12502,12489,12505,12977,14129,15001,21926,12978,12507,16177,16175,17380,16194,12986,12494,54368,12527,12483,16190,16409,12493,12501,12500,14960,14998,15002,12475,233274,12982,14969,16188,14961,14999",3.18357256127263e-32
|
| 30 |
+
"Apoptosis - Mus musculus (house mouse) Homo sapiens mmu04210",2.7074370755691e-33,"11651,11652,26395,13033,14939,64138,26420,53859,14281,13039,26419,13030,235587,21926,14102,13041,12364,12370,12633,12368,18033,18710,13347,16653,21937,13032,71609,11796,13036,13040,22146,12123,26413,16188,12983,12984,12045,12047,12044",3.18357256127263e-32
|
| 31 |
+
"IgSF CAM signaling - Mus musculus (house mouse) Homo sapiens mmu04517",4.36208962636793e-33,"16414,16402,11651,16822,11652,15170,17085,18106,26395,54631,30925,12506,18858,13822,66713,26420,26419,14083,13052,12524,67268,108100,16331,68507,18710,11867,243547,18479,16409,16411,17698,22324,234779,74053,17136,245450,243911,15894,18759,12523,75345,16456,17196,17096,22146,245446,241568,13384,19094,17528,26413,17974,13448",4.95824187530488e-32
|
| 32 |
+
"B cell receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04662",6.20892398634668e-33,"11651,11652,15170,26395,14281,19057,18037,83490,16331,14130,19055,18033,12517,18710,16653,12483,12229,18018,19354,19058,22324,234779,108723,12520,17096,18733,17060,14728,26413,232801,240168,14727",6.82981638498135e-32
|
| 33 |
+
"Coronavirus disease - Mus musculus (house mouse) Homo sapiens mmu05171",1.22903099639248e-32,"17857,16391,20848,13058,26420,14281,26419,17174,15976,17858,19106,12266,72512,12263,21926,15200,20846,71586,16194,24088,18033,18710,23961,21937,214763,17874,246727,246728,216799,234779,15945,20293,20296,100038882,12259,12262,12260,228607,21898,68172,20847,230073,12267,170743,12273,11491,246730,19094,14131,266632,26413,23960,100042335,12268,109828",1.30968615553074e-31
|
| 34 |
+
"Pertussis - Mus musculus (house mouse) Homo sapiens mmu05133",4.68510873290689e-32,"16414,16402,16362,26420,14281,26419,12258,12266,12263,21926,16175,18033,20311,16409,66824,17874,14678,216799,12259,12262,12260,107607,21898,15900,12475,19094,225471,14677,266632,26413,12268",4.84127902400379e-31
|
| 35 |
+
"TNF signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04668",6.33870155045936e-32,"11651,11652,26395,12977,16362,26420,217344,53859,14281,26419,56532,21926,14102,67457,12370,12633,18033,21938,18710,20311,21937,71609,11796,26398,15945,20304,20293,20296,67384,15894,11491,12702,19094,12051,26413,15953",6.35734479031365e-31
|
| 36 |
+
"Cell adhesion molecule (CAM) interaction - Mus musculus (house mouse) Homo sapiens mmu04514",8.47195476281161e-32,"16414,50723,14991,60533,20971,74048,14663,13052,12524,15001,12511,18566,19264,20612,12483,16409,171171,15015,14960,17136,245450,15894,18417,14998,16456,320840,15002,245446,56173,20345,241568,15039,17528,15018,14969,14972,15040,15007,110557,14964,14961,14999",8.25410449748217e-31
|
| 37 |
+
"Yersinia infection - Mus musculus (house mouse) Homo sapiens mmu05135",9.80652571311148e-31,"16402,11651,16822,20111,11652,26395,66713,26420,14281,26419,23880,14083,21926,108100,18033,18710,11867,16797,66824,22376,110651,17874,216799,18018,19354,26398,22324,20293,20296,21898,19094,54353,14131,266632,26413,56212,215280",9.28895907825282e-30
|
| 38 |
+
"Antigen processing and presentation - Mus musculus (house mouse) Homo sapiens mmu04612",2.83654500586862e-30,"14991,19141,15519,13039,13030,19186,18044,21356,15001,21355,21926,16149,65972,15015,14960,21354,14998,213233,13040,15002,15039,15018,14969,12010,14972,15040,15007,110557,14964,14961,14999",2.61422120811135e-29
|
| 39 |
+
"C-type lectin receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04625",3.76428215463519e-30,"11651,16391,11652,16985,16362,26420,53859,26419,18753,19057,21926,18034,12370,20846,332579,19055,18033,18710,56760,16653,18479,66824,216799,18018,13655,19058,234779,13654,20847,19094,12051,14127,26413,56644",3.37794793350158e-29
|
| 40 |
+
"T cell receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04660",4.87597187776745e-30,"11651,12502,16822,11652,15170,26395,51792,26420,53859,14281,26419,19057,13383,18037,21926,72930,18566,19264,19055,18033,18710,269643,21682,16653,16797,18479,12501,12500,18018,19058,22324,108723,19094,26413,17974",4.26334977004795e-29
|
| 41 |
+
"Th1 and Th2 cell differentiation - Mus musculus (house mouse) Homo sapiens mmu04658",6.53993404020482e-30,"12502,14462,15979,26420,14281,26419,19057,15980,18037,15001,20846,19055,18033,16797,16190,16186,16453,270118,12501,12500,18018,19058,14960,14998,15002,19094,14969,26413,16185,14961,14999",5.43931099441425e-29
|
| 42 |
+
"PD-L1 expression and PD-1 checkpoint pathway in cancer - Mus musculus (house mouse) Homo sapiens mmu05235",6.53993404020482e-30,"11651,12502,20848,11652,15170,26395,60533,15979,15251,14281,19057,15980,18037,20846,18566,24088,19055,18033,18710,16653,16797,12501,12500,17874,18018,19058,21898,74481,19094,225471,26413",5.43931099441425e-29
|
| 43 |
+
"Viral carcinogenesis - Mus musculus (house mouse) Homo sapiens mmu05203",1.43068825249394e-29,"16391,20848,79221,107995,14991,15182,12534,22631,13383,19106,12266,18034,12566,54123,12370,20684,227753,19650,18033,242341,18710,16653,17000,16453,71609,13655,15015,13654,12571,17096,15039,319181,15018,319158,69386,14972,26413,15040,15007,319190,319161,110557,14964,12774",1.15822395690568e-28
|
| 44 |
+
"NF-kappa B signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04064",1.46051701310686e-29,"217069,16803,20303,53859,18792,21926,18034,12633,16177,21934,18033,17000,21937,16797,12229,24099,71609,11796,17874,234779,108723,15894,21898,230073,17096,12475,225471,266632,17060,100504346,12045,12047,12044",1.15822395690568e-28
|
| 45 |
+
"JAK-STAT signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04630",5.64007191697725e-28,"11651,16391,20848,11652,15170,19116,50931,16164,15979,216233,14580,18414,17869,15980,16155,15976,20846,16194,18710,12986,60504,16190,16186,16453,16154,12700,57914,56468,12703,20847,12702,18413,12982,16185,16188,12983,12984,12803",4.37105573565737e-27
|
| 46 |
+
"AGE-RAGE signaling pathway in diabetic complications - Mus musculus (house mouse) Homo sapiens mmu04933",8.69829833943995e-28,"11651,20848,11652,21812,13058,26420,72469,26419,18753,21926,74055,20846,18802,16175,18033,18710,18762,16653,11606,21813,18018,234779,20293,20296,15894,13653,18796,19094,26413,12829,12828",6.59137718610894e-27
|
| 47 |
+
"Hepatitis B - Mus musculus (house mouse) Homo sapiens mmu05161",1.56769237912602e-27,"11651,20848,11652,26395,21812,26420,14281,26419,22631,17869,21926,14102,12566,54123,12364,12370,20846,71586,24088,18033,18710,16653,16453,21813,17874,18018,26398,13655,228607,13654,21898,20847,230073,19094,225471,266632,26413",1.16213717669994e-26
|
| 48 |
+
"Fc gamma R-mediated phagosome formation - Mus musculus (house mouse) Homo sapiens mmu04666",1.63718348946169e-27,"11651,15162,11652,26395,14129,17969,66713,218038,19012,18753,16331,19264,14130,227753,18710,11867,22323,16797,18479,22376,19354,22324,234779,230837,17096,50784,18783,246256,14131,26413",1.18782887214136e-26
|
| 49 |
+
"Neutrophil extracellular trap formation - Mus musculus (house mouse) Homo sapiens mmu04613",1.0147293327207e-26,"16414,12727,11651,11652,12725,79221,26395,13057,13058,14129,17969,15182,404634,22333,69146,12266,17970,24088,18033,18710,16409,19354,12363,234779,21898,18796,170743,20345,12273,19094,319181,246256,14131,319158,69386,26413,319190,319161,17972,56644",7.20880630120329e-26
|
| 50 |
+
"Efferocytosis - Mus musculus (house mouse) Homo sapiens mmu04148",1.75619685280831e-26,"26362,15170,26395,11303,171285,15251,12325,14083,16419,19128,16889,11689,68365,17304,11937,319520,192654,18018,240672,70839,12259,12262,12260,18218,19219,21825,233571,12642,13051,18514,11491,226421,19094,235584,26413,228432",1.22216964654619e-25
|
| 51 |
+
"Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse) Homo sapiens mmu04061",5.17623688798422e-26,"20302,12977,20305,20303,20308,16155,55985,21926,12978,16174,16963,16194,21938,20311,17329,17000,21937,16186,76527,16154,15945,20304,20293,20296,12766,13051,16185,100504346,12774",3.53019355760524e-25
|
| 52 |
+
"Rheumatoid arthritis - Mus musculus (house mouse) Homo sapiens mmu05323",6.82986824242273e-26,"16414,20302,27060,12977,11974,14281,13039,11600,12524,15001,21926,21934,16175,24088,242341,20311,24099,20304,20293,20296,14960,15894,14998,21898,15002,14969,14961,14999",4.56663739346304e-25
|
| 53 |
+
"Platelet activation - Mus musculus (house mouse) Homo sapiens mmu04611",9.46712286106975e-26,"11651,16822,11652,30955,320207,210044,67268,108101,54519,20619,21894,18710,18762,21391,54368,22323,12229,11513,14678,234779,70839,18759,18796,17096,19224,22320,19094,18783,14677,14127,14131,26413",6.20824787620151e-25
|
| 54 |
+
"Rap1 signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04015",2.91287323116089e-25,"16414,11651,16822,11652,26395,56044,12977,16000,210044,23880,11600,12978,74055,54519,13638,21894,18710,18762,16653,22323,16797,16409,11601,11513,71785,14678,19354,22324,14164,14173,18759,18796,21825,19094,20469,14677,26413,381810,240168",1.87413164495446e-24
|
| 55 |
+
"Necroptosis - Mus musculus (house mouse) Homo sapiens mmu04217",3.69248517358231e-25,"16391,20848,13058,15979,404634,26420,22333,15519,12325,26419,56532,15980,15976,19106,21926,14319,14102,77125,12370,12633,20846,16175,58203,21937,66824,16453,71609,11796,216799,78779,21898,20847,14325,225471,18783,434624",2.33173600776216e-24
|
| 56 |
+
"Proteoglycans in cancer - Mus musculus (house mouse) Homo sapiens mmu05205",5.17895735092886e-25,"16402,11651,20848,11652,15170,26395,12505,20971,16000,15251,13039,12325,18792,17869,14083,16419,15163,21926,15200,14102,18569,74055,12512,22409,24088,18710,16653,18479,17698,22324,234779,15442,14173,21898,21825,18793,19094,26413",3.21095355757589e-24
|
| 57 |
+
"Cellular senescence - Mus musculus (house mouse) Homo sapiens mmu04218",8.35245998037248e-25,"11651,11652,26395,21812,215999,63873,14991,103213,12534,22333,19057,17869,12566,16175,19650,19055,18033,18710,50883,16653,13685,12442,21813,18018,19058,15015,12571,19094,15039,15018,14972,26413,15040,15007,110557,14964",5.08605152376253e-24
|
| 58 |
+
"Sphingolipid signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04071",5.5493212540743e-24,"14673,11542,11651,11652,26395,51792,13033,76893,20397,26420,20773,12062,26419,21926,72930,66844,18033,18710,18762,269643,16653,21937,11886,71609,14678,19354,18796,19094,14677,14127,26413",3.31985710112164e-23
|
| 59 |
+
"Prolactin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04917",7.07091763619115e-24,"21823,11651,20848,11652,26395,19116,16362,216233,26420,14281,26419,20846,21934,18033,12640,18710,16653,12700,56468,12703,20416,12702,19094,26413,16866",4.15721192058824e-23
|
| 60 |
+
"Neuroactive ligand-receptor interaction - Mus musculus (house mouse) Homo sapiens mmu04080",1.11628634996037e-23,"11542,19116,12921,14399,18217,12062,108068,12266,14823,11516,14802,319229,18429,11550,18167,12640,12425,18439,18438,109648,12426,14396,108043,11606,67168,14402,15558,110312,74191,30878,381677,11998,19219,12267,12257,15171,243764,20606,233571,12273,12918,58861,140498,213438,110886,19204,12802,268934,16866",6.45175670061839e-23
|
| 61 |
+
"Complement and coagulation cascades - Mus musculus (house mouse) Homo sapiens mmu04610",1.58543801585797e-23,"16414,12062,18792,12759,15160,17174,19128,12258,12266,12263,20720,12628,21788,19124,232345,16409,16411,14071,12259,12262,12260,18816,12267,18793,12273,12268,109828",9.01057272345944e-23
|
| 62 |
+
"cAMP signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04024",1.72753706618348e-23,"11651,11652,26395,12921,26420,14281,210044,12325,26419,11516,74055,14802,12292,11931,18429,18033,12640,18710,109648,18576,11937,18479,11513,110385,11933,14678,18018,19354,22324,56188,80885,243764,20606,12064,12918,14677,26413,16866",9.65721540276339e-23
|
| 63 |
+
"Calcium signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04020",2.49626187287681e-23,"215999,215303,22333,72469,12062,210044,12325,19057,14675,74055,18802,12292,11550,19055,12494,12425,18439,18438,11937,12426,11513,71785,18018,19058,234779,14672,14676,15558,14164,102093,14173,320404,116873,18796,269999,243764,233979,58861,19204,18573",1.37294403008225e-22
|
| 64 |
+
"HIF-1 signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04066",3.78353349673102e-23,"15277,21857,11651,20848,11652,13807,26395,15368,13058,15979,16000,15251,56421,12325,11600,15980,212032,16194,18033,18710,17346,17000,18597,11601,13685,22041,234779,21898,26413",2.015913941227e-22
|
| 65 |
+
"Growth hormone synthesis, secretion and action - Mus musculus (house mouse) Homo sapiens mmu04935",3.78353349673102e-23,"11651,20848,11652,26395,216233,16000,26420,14281,210044,26419,14083,20846,12292,18710,16653,11513,14678,26398,234779,14672,12703,18796,20416,20606,12702,19094,16370,14677,26413",2.015913941227e-22
|
| 66 |
+
"Type I diabetes mellitus - Mus musculus (house mouse) Homo sapiens mmu04940",1.2821700557637e-22,"14939,14991,12524,15001,21926,14102,16175,15015,14960,14998,15002,15039,15018,14969,14972,15893,15040,15007,14415,110557,14964,14961,14999",6.72646136946802e-22
|
| 67 |
+
"Fc epsilon RI signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04664",1.92979512141877e-22,"11651,16822,11652,26395,26420,26419,21926,11689,16331,18710,16653,16797,12229,19354,26398,22324,234779,17096,19094,18783,14127,11690,26413",9.97060812733032e-22
|
| 68 |
+
"Fluid shear stress and atherosclerosis - Mus musculus (house mouse) Homo sapiens mmu05418",3.48436809851739e-22,"11651,11652,15368,13057,63873,18024,17969,20971,26420,14281,15519,13039,26419,14083,19252,21926,16177,17970,11477,16175,18033,108079,18710,18762,21937,19354,26398,20293,20296,15894,19094",1.77338734566333e-21
|
| 69 |
+
"Insulin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04910",6.53437889179828e-22,"15277,11651,19088,11652,26395,23921,20528,216233,26420,26419,19085,212032,108079,18710,17346,18762,16653,18576,13685,68401,102093,18759,12703,20416,140491,244416,12702,16370,26413,14121",3.27679882662237e-21
|
| 70 |
+
"Alcoholic liver disease - Mus musculus (house mouse) Homo sapiens mmu04936",8.13833338399454e-22,"11651,11652,16803,26420,53859,26419,12266,12263,21926,14102,21416,13106,12370,18033,108079,207565,21937,71609,17874,26398,12259,12262,12260,21898,12267,12273,12475,19094,266632,12268",4.02198794774223e-21
|
| 71 |
+
"Inflammatory bowel disease - Mus musculus (house mouse) Homo sapiens mmu05321",9.94857613461502e-22,"20848,14462,15979,15980,15001,21926,16174,20846,16175,24088,18033,60504,16190,16186,18018,14960,14998,21898,15002,14969,14961,14999",4.8463778027196e-21
|
| 72 |
+
"Alzheimer disease - Mus musculus (house mouse) Homo sapiens mmu05010",2.28621598179722e-21,"11651,11816,74764,11652,26395,215999,12977,13058,16956,26420,22333,68585,16593,26419,19057,19106,21926,93687,14102,12364,12370,22409,12292,16175,17380,56811,19055,18033,18710,16653,21937,11937,12862,19058,73677,11785,18796,69806,22146,30791,11491,16370,72027,26413,14296,12865",1.09802767576458e-20
|
| 73 |
+
"cGMP-PKG signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04022",2.7740299153652e-21,"14673,11542,11651,11652,26395,17540,16533,22333,30955,320207,12062,210044,19057,12292,11931,11550,19055,22323,18576,11937,11513,11933,14678,18018,19058,14672,72413,18796,242202,16370,14677,26413",1.31381139047158e-20
|
| 74 |
+
"Phospholipase D signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04072",4.41084246404156e-21,"14673,11651,19158,11652,26395,56044,72318,30955,320207,210044,19012,108068,14823,67512,18710,16653,11513,11606,71785,67168,234779,11998,18796,20416,50784,18783,14127,268934,26413,381810",2.06040723320297e-20
|
| 75 |
+
"Graft-versus-host disease - Mus musculus (house mouse) Homo sapiens mmu05332",5.07173438581654e-21,"14939,14991,12524,15001,21926,14102,16175,15015,14960,14998,15002,15039,15018,14969,14972,15040,15007,110557,14964,14961,14999",2.33711003454519e-20
|
| 76 |
+
"Cytoskeleton in muscle cells - Mus musculus (house mouse) Homo sapiens mmu04820",6.39734504024394e-21,"16402,12833,53867,13807,21393,14200,20971,109272,30794,213019,16419,22379,17929,13506,21952,11931,22352,17996,12841,21827,54418,21894,21953,326618,22003,11933,14201,21825,118449,54132,21955,12829,68794,12335,12828,667772",2.90865954496425e-20
|
| 77 |
+
"Ras signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04014",1.14773923179688e-20,"11651,11652,26395,54153,56044,12977,16000,26420,26419,11600,12978,74055,13638,18033,18710,14688,72399,16653,16797,18479,11601,71785,19354,234779,14164,14173,14710,18784,19732,20416,12064,320484,18783,26413,14707,240168",5.14972471108861e-20
|
| 78 |
+
"Endocytosis - Mus musculus (house mouse) Homo sapiens mmu04144",1.17115179634636e-20,"19158,21812,71889,14991,72318,66713,218038,13132,98366,227700,215632,98878,20404,72685,140500,18762,11867,16186,69091,21813,14276,69710,15015,230837,54673,73728,100017,18759,15039,15018,14972,15040,15007,16185,110557,14964,215280,12774",5.18652938381958e-20
|
| 79 |
+
"Relaxin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04926",1.61598870577948e-20,"11651,11652,26395,21812,26420,14281,210044,26419,18033,18710,18762,14688,16653,11513,21813,14678,26398,14676,14710,18796,20416,19094,140498,14677,26413,12829,14707,12828",7.06477113680515e-20
|
| 80 |
+
"Transcriptional misregulation in cancer - Mus musculus (house mouse) Homo sapiens mmu05202",6.55616551643516e-20,"20375,104156,14939,14129,14247,15182,16000,18792,17869,14083,12524,12394,12978,15242,20732,18033,18124,16409,15446,11796,21813,17095,20474,140780,12606,269397,545192,12475,18514,21912,16185,12045,12047,12044",2.82993979886631e-19
|
| 81 |
+
"Allograft rejection - Mus musculus (house mouse) Homo sapiens mmu05330",1.35613709163516e-19,"14939,14991,12524,15001,21926,14102,15015,14960,14998,15002,15039,15018,14969,14972,15040,15007,110557,14964,14961,14999",5.78053435309488e-19
|
| 82 |
+
"Leukocyte transendothelial migration - Mus musculus (house mouse) Homo sapiens mmu04670",2.05298885159507e-19,"16414,13057,13058,17969,14083,67268,17970,18710,74734,22323,16409,17698,21838,14678,19354,22324,234779,15894,18417,16456,56173,19094,20469,14677,216033,17972",8.64282960980148e-19
|
| 83 |
+
"Staphylococcus aureus infection - Mus musculus (house mouse) Homo sapiens mmu05150",2.11220659650539e-19,"16414,14129,17174,16668,12266,15001,12263,12628,14130,16409,14960,12259,12262,12260,15894,14998,12267,15002,20345,12273,19204,246256,14131,14969,12268,14961,14999",8.78368840741877e-19
|
| 84 |
+
"Acute myeloid leukemia - Mus musculus (house mouse) Homo sapiens mmu05221",4.62650802320484e-19,"11651,20375,20848,11652,26395,14129,17869,12394,12978,21416,18033,18710,16653,16409,13685,12606,12475,26413,12045,12047,12044",1.90077016375042e-18
|
| 85 |
+
"Cadherin signaling - Mus musculus (house mouse) Homo sapiens mmu04519",1.05321268409539e-18,"26395,66713,26420,14399,246177,59079,26419,22631,105855,14083,16668,17916,13506,93687,21416,217353,22409,22352,50884,18033,54216,11867,16653,22323,14396,12552,71602,19354,14402,22324,106042,74127,237091,232157,218454,18526,16691,20776,22601,19094,110886,216033,26413,12939",4.2755419675777e-18
|
| 86 |
+
"Oxytocin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04921",1.56456672917281e-18,"12297,26395,215303,12298,30955,320207,14281,210044,12325,19057,12292,16519,18429,19055,108079,12494,207565,16653,11513,14678,18018,19058,18796,12293,16518,18783,14677,26413",6.27667358409327e-18
|
| 87 |
+
"Autoimmune thyroid disease - Mus musculus (house mouse) Homo sapiens mmu05320",1.68138131989674e-18,"14939,14991,12524,15001,14102,12640,15015,14960,14998,15002,21819,15039,15018,14969,14972,15040,15007,110557,14964,14961,14999",6.66687244284636e-18
|
| 88 |
+
"Regulation of actin cytoskeleton - Mus musculus (house mouse) Homo sapiens mmu04810",4.58231233965682e-18,"14673,16414,16402,11651,11652,26395,66713,12062,219140,105855,14083,16419,67268,108100,227753,50884,404710,18710,11867,16653,18479,16409,16411,17698,71785,19354,22324,14164,14173,243764,26413,381810,109828",1.79605575611836e-17
|
| 89 |
+
"Axon guidance - Mus musculus (house mouse) Homo sapiens mmu04360",1.38918061633254e-17,"13845,20354,12325,19057,14083,67268,13638,19055,18710,18762,13848,16653,20352,18479,14678,319713,22063,19354,19058,234779,171171,11854,241568,14159,14677,20347,26413,20349,17974",5.38307488828858e-17
|
| 90 |
+
"Integrin signaling - Mus musculus (house mouse) Homo sapiens mmu04518",1.40915044566554e-17,"16414,16402,12833,11651,11652,110829,16000,64099,14083,16419,12266,108101,12841,21827,21894,18710,20750,16409,16411,71785,19354,15894,12643,21825,17974,12829,12828",5.39910451653877e-17
|
| 91 |
+
"Viral myocarditis - Mus musculus (house mouse) Homo sapiens mmu05416",1.48965766302555e-17,"16414,14991,13052,12524,15001,12370,19354,15015,14960,15894,14998,15002,15039,15018,14969,14972,15040,15007,110557,14964,14961,14999",5.6441473676857e-17
|
| 92 |
+
"Cytosolic DNA-sensing pathway - Mus musculus (house mouse) Homo sapiens mmu04623",1.74080658951735e-17,"13423,20303,56532,69146,72512,77125,54123,12370,70408,58203,18033,66824,214763,216799,15945,20304,228607,383619,230073,22040,15951",6.52324227500459e-17
|
| 93 |
+
"Progesterone-mediated oocyte maturation - Mus musculus (house mouse) Homo sapiens mmu04914",1.91347435958367e-17,"11651,20111,11652,26395,12534,16000,20868,26420,15519,210044,26419,12566,18710,16653,18576,110651,11513,12442,14678,19094,14677,26413",7.02031103942958e-17
|
| 94 |
+
"Chemical carcinogenesis - reactive oxygen species - Mus musculus (house mouse) Homo sapiens mmu05208",1.91463028348079e-17,"11651,57344,11652,26395,15368,13057,20656,76113,18024,17969,26420,22333,53859,15251,14281,26419,18753,14083,13106,17970,18033,18710,16653,12862,26398,384214,13521,13849,13107,19094,26413,12865",7.02031103942958e-17
|
| 95 |
+
"Glutamatergic synapse - Mus musculus (house mouse) Homo sapiens mmu04724",2.32621846103036e-17,"224997,26556,210044,19057,108068,14823,14802,14660,16519,19055,14688,140919,11513,14678,22063,19058,14710,18796,216456,18783,14677,268934,26413,14707",8.43872867246119e-17
|
| 96 |
+
"Hormone signaling - Mus musculus (house mouse) Homo sapiens mmu04081",4.73499438756163e-17,"14673,20848,19116,12921,16000,210044,14675,11477,18429,11550,12640,18710,14688,12425,12426,11513,11606,14678,14672,14676,110312,11998,14710,18796,15171,20606,12918,16370,14677,14707,16866",1.6996137749037e-16
|
| 97 |
+
"Pathways of neurodegeneration - multiple diseases - Mus musculus (house mouse) Homo sapiens mmu05022",5.73523293002421e-17,"74764,26395,215999,12977,13058,19324,26420,22333,16593,12325,26419,19057,67819,21926,93687,14102,12364,14802,12370,22409,12292,56791,16175,56811,19055,18033,21938,16653,21937,11937,12862,74153,19058,432611,73677,226977,18796,105000,75563,22146,12064,19094,26413,14296,12865",2.03720253035235e-16
|
| 98 |
+
"Cholesterol metabolism - Mus musculus (house mouse) Homo sapiens mmu04979",1.40531524367989e-16,"11816,11813,11303,16956,22333,67963,16889,104086,20652,14725,11814,15450,16816,100017,218203,11812,12257",4.94033503190559e-16
|
| 99 |
+
"Cholinergic synapse - Mus musculus (house mouse) Homo sapiens mmu04725",1.57422636689661e-16,"11651,11652,26395,30955,320207,14281,210044,12325,12292,16519,18710,14688,16653,11513,14678,14672,14710,18796,16518,243764,14677,26413,14707",5.47766521542595e-16
|
| 100 |
+
"Adrenergic signaling in cardiomyocytes - Mus musculus (house mouse) Homo sapiens mmu04261",2.37958784874646e-16,"11651,12297,11652,51792,12298,30955,320207,210044,12325,72930,12292,11931,11550,269643,11937,11513,326618,11606,22003,11933,14678,18796,12293,19094,14677,26413",8.19635814568225e-16
|
| 101 |
+
"Focal adhesion - Mus musculus (house mouse) Homo sapiens mmu04510",2.8731900175061e-16,"16402,12833,11651,11652,26395,16000,26420,26419,64099,14083,16419,67268,12841,21827,21894,18710,20750,22323,18479,11796,71785,19354,22324,12643,21825,20416,26413,12829,12828",9.79757795969579e-16
|
| 102 |
+
"Prion disease - Mus musculus (house mouse) Homo sapiens mmu05020",4.89088035621487e-16,"74764,13057,215999,13058,17969,26420,22333,16593,26419,18753,19057,21926,12364,12292,17970,16175,19055,18710,12862,19354,19058,20304,73677,12259,12262,12260,13653,22146,19094,26413,17972,12865,109828",1.6512774271973e-15
|
| 103 |
+
"Systemic lupus erythematosus - Mus musculus (house mouse) Homo sapiens mmu05322",8.87825354860552e-16,"14129,404634,12524,12266,15001,12263,21926,14960,12259,12262,12260,14998,15002,319181,246256,14131,14969,319158,69386,319190,319161,12268,14961,109828,14999",2.96812201968086e-15
|
| 104 |
+
"TGF-beta signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04350",1.2898400600084e-15,"15216,51792,21812,15903,15182,14313,17869,21926,269275,11477,19650,209268,21813,22041,21781,13590,21825,13732,21815,380664,224109,26413",4.27024718895984e-15
|
| 105 |
+
"FoxO signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04068",5.40343230780844e-15,"11651,20848,11652,26395,20656,21812,26556,18099,20528,16000,26420,20620,26419,12566,108079,18710,16653,12442,21813,68401,19094,16370,26413",1.76205929045017e-14
|
| 106 |
+
"Adipocytokine signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04920",5.42569576238322e-15,"11651,20848,11652,20528,26420,26419,18037,21926,18033,108079,21938,207565,109648,21937,71609,68401,12702,16370",1.76205929045017e-14
|
| 107 |
+
"Neurotrophin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04722",7.06083455485552e-15,"11651,20111,11652,26395,23921,26420,12325,26419,18753,18037,18033,18710,11857,16653,110651,234779,192656,20416,12064,19094,266632,26413",2.27145715396767e-14
|
| 108 |
+
"GnRH secretion - Mus musculus (house mouse) Homo sapiens mmu04929",7.64147500566098e-15,"11651,11652,26395,15165,12292,16519,15168,12640,18710,20750,16653,22063,14672,18796,140492,26413,16866",2.43527381021532e-14
|
| 109 |
+
"Neuroactive ligand signaling - Mus musculus (house mouse) Homo sapiens mmu04082",8.51734310090692e-15,"11542,14399,210044,108068,14823,14802,11550,14688,18438,140919,14396,11513,15561,14678,14402,14672,15558,70839,74191,14710,18796,243764,233571,110886,14677,268934,14707",2.68927221982339e-14
|
| 110 |
+
"Insulin resistance - Mus musculus (house mouse) Homo sapiens mmu04931",1.03579406450291e-14,"11651,20111,20848,11652,58805,20528,26420,26419,18753,21926,18033,108079,18710,18762,21937,110651,11606,68401,140491,244416,12702",3.24041996326141e-14
|
| 111 |
+
"Autophagy - animal - Mus musculus (house mouse) Homo sapiens mmu04140",1.16949230947527e-14,"11651,11652,52440,26395,13033,16784,19324,26420,15251,13039,26419,13030,18753,97998,12633,108079,242557,18710,207565,16653,54673,22320,226421,16370,26413",3.62542615937333e-14
|
| 112 |
+
"Diabetic cardiomyopathy - Mus musculus (house mouse) Homo sapiens mmu05415",1.31903174969985e-14,"11651,11652,13057,21812,13033,13058,17969,20528,26420,22333,12325,26419,18753,17970,18033,12896,18710,18762,11937,12862,18597,11606,21813,19354,18796,19094,17972,12865",4.05216060042928e-14
|
| 113 |
+
"Sphingolipid metabolism - Mus musculus (house mouse) Homo sapiens mmu00600",1.73967693706546e-14,"14667,76893,20397,20773,15212,19012,15211,14466,22234,66190,11886,22239,241159,12091,50784,56386",5.29669496017252e-14
|
| 114 |
+
"GnRH signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04912",2.73863251976145e-14,"26395,26420,210044,12325,26419,18753,15200,12292,12640,16653,11513,26398,14672,13653,18796,19094,18783,26413,16866",8.26436893131554e-14
|
| 115 |
+
"Legionellosis - Mus musculus (house mouse) Homo sapiens mmu05134",4.3252699411755e-14,"16414,19324,12266,21926,18034,12370,24088,18033,16409,66824,17874,21898,12475,17951,17952,17948",1.29378688591302e-13
|
| 116 |
+
"Intestinal immune network for IgA production - Mus musculus (house mouse) Homo sapiens mmu04672",9.82116142505938e-14,"50723,57916,53859,21935,12524,15001,17000,24099,14960,14998,15002,14969,14961,14999",2.90140214730808e-13
|
| 117 |
+
"ErbB signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04012",9.86987240726503e-14,"11651,11652,26395,26420,12325,26419,17869,14083,15200,18710,16653,18479,13685,26398,234779,20416,26413,17974",2.90140214730808e-13
|
| 118 |
+
"Dopaminergic synapse - Mus musculus (house mouse) Homo sapiens mmu04728",1.02090979609223e-13,"21823,11651,11652,51792,26420,14281,12325,26419,19057,72930,14802,16519,19055,14688,269643,14678,14710,18796,19094,11865,14677,14707",2.97547214074745e-13
|
| 119 |
+
"Choline metabolism in cancer - Mus musculus (house mouse) Homo sapiens mmu05231",1.41429681205156e-13,"11651,11652,26395,30805,26420,15251,14281,19012,26419,12660,18710,16653,22376,13685,71785,19354,50784,18783,26413",4.08707807550492e-13
|
| 120 |
+
"Apelin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04371",1.61457981450716e-13,"11651,11652,26395,21812,14219,30955,320207,210044,108079,14688,20750,16653,18576,11513,14678,30878,13653,14710,18796,14677,26413,14707",4.62665308190707e-13
|
| 121 |
+
"Wnt signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04310",4.69223075286559e-13,"22402,18099,54612,72780,14160,26420,12325,26419,19057,17869,93687,21416,22409,56811,19055,18018,19354,19058,106042,18796,329252,107515,239405,14296",1.33337557227264e-12
|
| 122 |
+
"Other glycan degradation - Mus musculus (house mouse) Homo sapiens mmu00511",4.77797958650861e-13,"17159,66848,15212,15211,14466,71665,17160,11593,241159,12091",1.34652151983424e-12
|
| 123 |
+
"Type II diabetes mellitus - Mus musculus (house mouse) Homo sapiens mmu04930",5.49244912913205e-13,"15277,20528,216233,26420,26419,18753,21926,212032,18710,18762,12703,12702,16370,26413",1.53518455166724e-12
|
| 124 |
+
"VEGF signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04370",5.78431915118163e-13,"11651,11652,26395,19057,14083,19055,18710,16653,102626,19354,19058,234779,19094,18783,26413",1.60362018744141e-12
|
| 125 |
+
"Central carbon metabolism in cancer - Mus musculus (house mouse) Homo sapiens mmu05230",6.22099215160713e-13,"15277,11651,20514,11652,26395,15251,56421,17869,80879,212032,14660,18710,16653,18597,216456,26413",1.71077284169196e-12
|
| 126 |
+
"Thyroid hormone signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04919",6.46957591188656e-13,"11651,11652,26395,15182,72469,15251,56421,17869,74055,20846,18802,11931,18710,16653,11937,11933,234779,53901,18796,26413",1.76490030876265e-12
|
| 127 |
+
"Serotonergic synapse - Mus musculus (house mouse) Homo sapiens mmu04726",9.39890374386714e-13,"26395,19252,11689,12292,16519,14688,16653,15561,14678,22063,14402,15558,14710,18796,81906,19224,140492,18783,14677,26413,14707",2.54367156877674e-12
|
| 128 |
+
"Tight junction - Mus musculus (house mouse) Homo sapiens mmu04530",1.03741159856939e-12,"51792,66713,26420,26419,13383,15163,12394,67268,72930,108079,18762,269643,11867,22323,22376,17698,27375,231830,18417,18759,16456,22146,56173",2.78549098513513e-12
|
| 129 |
+
"RIG-I-like receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04622",1.58709923030435e-12,"217069,80861,26420,26419,72512,21926,54123,12370,71586,18033,71609,15945,100038882,228607,230073,19094",4.22813154323269e-12
|
| 130 |
+
"Alcoholism - Mus musculus (house mouse) Homo sapiens mmu05034",1.86960270100562e-12,"21823,14282,79221,26395,15182,404634,71279,63959,14688,207565,109648,16653,14678,14710,20416,12064,12918,14677,319181,319158,69386,26413,14707,319190,319161",4.94212807010012e-12
|
| 131 |
+
"Hippo signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04390",2.00310375241039e-12,"16414,51792,21812,14219,22631,17869,20583,13383,72930,21416,22409,18762,269643,11796,21813,14164,18759,232157,319710,22601,11576,216033",5.25429522747649e-12
|
| 132 |
+
"Pancreatic cancer - Mus musculus (house mouse) Homo sapiens mmu05212",3.07750947790352e-12,"11651,20848,11652,26395,21812,56044,26420,26419,20846,18033,18710,16653,21813,19354,12571,26413",8.01092161805419e-12
|
| 133 |
+
"Glycosaminoglycan degradation - Mus musculus (house mouse) Homo sapiens mmu00531",3.64145608418791e-12,"27419,15212,15211,110006,15932,75612,15442,109685,52120,12091",9.4070948841521e-12
|
| 134 |
+
"Motor proteins - Mus musculus (house mouse) Homo sapiens mmu04814",4.28243913107307e-12,"74764,16551,246177,16593,67268,17916,21952,16579,228421,13426,21953,16582,326618,71602,22003,432611,226977,105000,75563,22146,103768,21955,667772,100041586",1.09797875465858e-11
|
| 135 |
+
"Oocyte meiosis - Mus musculus (house mouse) Homo sapiens mmu04114",9.74639384177702e-12,"20111,26395,107995,51792,12534,16000,210044,12325,19057,22631,12566,19055,110651,11513,12442,19058,50878,19094,26413",2.48023902988505e-11
|
| 136 |
+
"Long-term depression - Mus musculus (house mouse) Homo sapiens mmu04730",1.57043649113451e-11,"14673,26395,51792,12921,16000,16653,14678,14672,18796,17096,12918,18783,14677,26413",3.9668062479768e-11
|
| 137 |
+
"Chemical carcinogenesis - receptor activation - Mus musculus (house mouse) Homo sapiens mmu05207",1.91624256193048e-11,"11651,20111,20848,11652,26395,14281,15519,210044,17869,12292,18033,18710,16653,110651,13685,11513,14678,384214,14173,13849,94284,14677,26413,13090,394432",4.80469642366394e-11
|
| 138 |
+
"Non-alcoholic fatty liver disease - Mus musculus (house mouse) Homo sapiens mmu04932",2.53363532896456e-11,"11651,11652,58805,26420,14281,26419,21926,14102,13106,12370,16175,16194,18033,108079,18710,21937,12862,12606,12702,19094,12865",6.30634778961251e-11
|
| 139 |
+
"Colorectal cancer - Mus musculus (house mouse) Homo sapiens mmu05210",3.26579101516989e-11,"11651,11652,26395,21812,56044,26420,14281,26419,17869,17685,21416,18710,16653,21813,19354,26413",8.06981692878936e-11
|
| 140 |
+
"Estrogen signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04915",4.54951784874809e-11,"11651,11652,26395,13033,14281,15519,210044,18753,16668,15200,16519,18710,16653,11513,14678,18796,20416,14677,26413",1.11610473843388e-10
|
| 141 |
+
"Cornified envelope formation - Mus musculus (house mouse) Homo sapiens mmu04382",4.91282798508254e-11,"20198,20200,54325,51792,20773,21816,16668,72930,20195,14466,22234,269643,19143,83603,74127,18417,19041,386463,20193,56173,16691,12829,67860,12828",1.19662453065225e-10
|
| 142 |
+
"GABAergic synapse - Mus musculus (house mouse) Homo sapiens mmu04727",5.5461635104456e-11,"14399,210044,14660,12292,14688,14396,11513,14678,14402,14710,216456,268566,110886,14677,14707,14415",1.34130621068223e-10
|
| 143 |
+
"Malaria - Mus musculus (house mouse) Homo sapiens mmu05144",6.24995679129593e-11,"16414,21926,24088,21827,17059,17057,17874,20293,20296,15894,12520,21898,21825,80782",1.50086990551543e-10
|
| 144 |
+
"Mineral absorption - Mus musculus (house mouse) Homo sapiens mmu04978",6.99428127964152e-11,"15368,14319,11931,73649,17750,17748,11933,22041,333669,14325,434624,72027,20529",1.66786707437606e-10
|
| 145 |
+
"Retrograde endocannabinoid signaling - Mus musculus (house mouse) Homo sapiens mmu04723",7.22906597506164e-11,"26420,14399,210044,26419,14802,12292,16519,14688,140919,14396,11513,14678,14402,14710,18796,19094,110886,14677,26413,14707",1.71188298437224e-10
|
| 146 |
+
"Amoebiasis - Mus musculus (house mouse) Homo sapiens mmu05146",7.48734086154e-11,"16414,14083,21926,14675,16177,24088,18033,18710,16409,14672,14676,21898,18796,12475,226421,12829,12828",1.7608160233001e-10
|
| 147 |
+
"Primary immunodeficiency - Mus musculus (house mouse) Homo sapiens mmu05340",9.70011284433833e-11,"57916,21355,19264,22256,12229,16186,16453,12501,12500,21354,17060",2.26557430131464e-10
|
| 148 |
+
"AMPK signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04152",1.47211969341995e-10,"11651,11652,51792,20528,16000,56421,72930,270198,68365,108079,18710,269643,207565,13685,68401,12283,16370,14121",3.41491711194695e-10
|
| 149 |
+
"IL-17 signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04657",1.50475354787807e-10,"14282,103213,26420,14281,15519,26419,21926,12370,18033,20311,71609,15945,20293,20296,19094,26413",3.46703351234069e-10
|
| 150 |
+
"MicroRNAs in cancer - Mus musculus (house mouse) Homo sapiens mmu05206",1.64665656175391e-10,"16402,20848,26395,12505,15368,15182,18792,24064,17869,67849,18569,14660,22352,13638,18033,18710,18669,16653,19143,22003,234779,12703,21825,12571,20416,216456,26413,20677",3.76852273528914e-10
|
| 151 |
+
"Cushing syndrome - Mus musculus (house mouse) Homo sapiens mmu04934",1.82141016089514e-10,"26395,12921,210044,12325,21416,12566,22409,12292,11513,11606,14678,14672,18796,12571,16527,12918,19416,18514,14677,26413",4.14067243243495e-10
|
| 152 |
+
"Inflammatory mediator regulation of TRP channels - Mus musculus (house mouse) Homo sapiens mmu04750",2.18061938277614e-10,"63873,16000,26420,11418,12062,210044,12325,26419,18753,16177,18710,11513,234779,15558,19219,18796,19094,18783",4.92444509620307e-10
|
| 153 |
+
"Amino sugar and nucleotide sugar metabolism - Mus musculus (house mouse) Homo sapiens mmu00520",2.55770319733112e-10,"15277,15212,29858,15211,212032,107652,227620,229688,19703,245847,26384",5.73800519927573e-10
|
| 154 |
+
"Parathyroid hormone synthesis, secretion and action - Mus musculus (house mouse) Homo sapiens mmu04928",2.77234400166648e-10,"14673,26395,14462,14281,210044,15200,18227,17391,11513,110385,14678,14672,13653,18796,14677,26413,16658",6.17888434358347e-10
|
| 155 |
+
"Gastric cancer - Mus musculus (house mouse) Homo sapiens mmu05226",3.3034380385013e-10,"11651,11652,26395,21812,17869,93687,21416,12566,22409,18710,18669,16653,21813,14164,14173,20416,216033,26413,14296",7.31475565668146e-10
|
| 156 |
+
"Renin secretion - Mus musculus (house mouse) Homo sapiens mmu04924",3.81208414321823e-10,"13030,19057,11516,12292,19055,18576,11606,14678,19058,19219,18796,16518,14677,18573",8.38658511508012e-10
|
| 157 |
+
"Glucagon signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04922",4.40165116565148e-10,"11651,11652,56421,210044,12325,19057,17691,19055,108079,18576,18597,19058,68401,102093,18796,14121",9.62155799671252e-10
|
| 158 |
+
"Chronic myeloid leukemia - Mus musculus (house mouse) Homo sapiens mmu05220",4.58458184249154e-10,"11651,11652,26395,21812,15182,17869,12394,18033,18710,16653,21813,12571,20416,26413",9.9575949572587e-10
|
| 159 |
+
"Prostate cancer - Mus musculus (house mouse) Homo sapiens mmu05215",6.78884426191769e-10,"11651,11652,26395,104156,16000,15519,18792,21416,12566,20732,18033,18710,16653,71785,14276,26413",1.46518727424933e-09
|
| 160 |
+
"Morphine addiction - Mus musculus (house mouse) Homo sapiens mmu05032",7.76424729544767e-10,"14399,210044,16519,14688,18576,14396,11513,110385,14678,14402,14710,110886,14677,18573,14707",1.66516247028154e-09
|
| 161 |
+
"mTOR signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04150",8.08633468178271e-10,"11651,20111,11652,26395,16000,71962,97998,21926,22409,108079,18710,16653,21937,110651,13685,72446,12283,329679,26413",1.72340007905494e-09
|
| 162 |
+
"Asthma - Mus musculus (house mouse) Homo sapiens mmu05310",9.44895912604842e-10,"15001,21926,14960,14998,15002,14127,14969,14961,14999",2.00130128073448e-09
|
| 163 |
+
"Vascular smooth muscle contraction - Mus musculus (house mouse) Homo sapiens mmu04270",1.18878329676478e-09,"14673,26395,17540,16533,210044,18753,12292,11550,11513,11606,14672,68458,72413,11998,18796,18784,18783,26413",2.50231545800489e-09
|
| 164 |
+
"Regulation of lipolysis in adipocytes - Mus musculus (house mouse) Homo sapiens mmu04923",1.58901334221195e-09,"11651,11652,210044,12640,18710,109648,18576,11513,14678,19224,16370,14677",3.32425490609985e-09
|
| 165 |
+
"Breast cancer - Mus musculus (house mouse) Homo sapiens mmu05224",1.66490994141701e-09,"11651,11652,26395,16000,14281,17869,93687,21416,18034,22409,18710,16653,14164,14173,12571,20416,26413,14296",3.46179445136099e-09
|
| 166 |
+
"Circadian entrainment - Mus musculus (house mouse) Homo sapiens mmu04713",2.20236050983408e-09,"14281,210044,12325,11516,14802,16519,14688,11513,14678,14710,18796,19416,14677,26413,14707",4.5515450536571e-09
|
| 167 |
+
"Gap junction - Mus musculus (house mouse) Homo sapiens mmu04540",2.50191116062776e-09,"26395,12534,210044,16653,11513,71785,14678,14672,15558,18796,22146,14677,26413,14617",5.10869284894651e-09
|
| 168 |
+
"Insulin secretion - Mus musculus (house mouse) Homo sapiens mmu04911",2.50191116062776e-09,"16533,22318,210044,12325,11516,12292,11931,12425,11513,11933,14672,72413,18796,140492",5.10869284894651e-09
|
| 169 |
+
"Glycerophospholipid metabolism - Mus musculus (house mouse) Homo sapiens mmu00564",2.9186179623495e-09,"19012,14555,12660,68671,67512,74596,192654,270084,16816,233552,241274,18784,50784,104759,18783",5.92409955453083e-09
|
| 170 |
+
"Longevity regulating pathway - multiple species - Mus musculus (house mouse) Homo sapiens mmu04213",3.62910434616577e-09,"11651,11652,20656,15182,16000,210044,108079,18710,16653,11513,12955,16370",7.32263066297353e-09
|
| 171 |
+
"Ether lipid metabolism - Mus musculus (house mouse) Homo sapiens mmu00565",3.68517523642255e-09,"67893,19012,18606,68616,22239,270084,320981,18784,50784,104759,18783",7.34879974046836e-09
|
| 172 |
+
"Carbohydrate digestion and absorption - Mus musculus (house mouse) Homo sapiens mmu04973",3.68517523642255e-09,"15277,11651,11652,212032,11931,18710,56485,11933,333669,68401,18796",7.34879974046836e-09
|
| 173 |
+
"ECM-receptor interaction - Mus musculus (house mouse) Homo sapiens mmu04512",3.97394426757199e-09,"16402,12833,12505,20971,16419,12841,21827,20750,54368,12643,21825,64176,12829,12828",7.87857555373284e-09
|
| 174 |
+
"Hepatocellular carcinoma - Mus musculus (house mouse) Homo sapiens mmu05225",4.54528865765275e-09,"11651,11652,26395,15368,21812,18024,17869,93687,21416,22409,18710,16653,29861,21813,234779,12571,20416,26413,14296",8.95921059109588e-09
|
| 175 |
+
"Signaling pathways regulating pluripotency of stem cells - Mus musculus (house mouse) Homo sapiens mmu04550",5.32407691226303e-09,"11651,20848,11652,26395,15903,16000,17869,22409,269275,11477,18710,16653,16453,14173,13590,19094,26413",1.04339668223086e-08
|
| 176 |
+
"Inositol phosphate metabolism - Mus musculus (house mouse) Homo sapiens mmu00562",5.83214877153196e-09,"53332,30955,72469,271424,17330,74055,18802,16331,327655,234779,170835,320404,18796",1.13643584633851e-08
|
| 177 |
+
"Glycosphingolipid biosynthesis - ganglio series - Mus musculus (house mouse) Homo sapiens mmu00604",8.32046735327222e-09,"15212,15211,225742,50935,26938,12091,20454",1.61209054969649e-08
|
| 178 |
+
"Galactose metabolism - Mus musculus (house mouse) Homo sapiens mmu00052",1.14004312231722e-08,"15277,56421,212032,14595,14187,68401,12091,67861,76051",2.19635426389928e-08
|
| 179 |
+
"Purine metabolism - Mus musculus (house mouse) Homo sapiens mmu00230",1.8965260338312e-08,"23917,11565,229589,210044,11636,229363,18576,11513,110385,78801,210808,12495,242202,14544,18573,18950",3.63323245806988e-08
|
| 180 |
+
"Dilated cardiomyopathy - Mus musculus (house mouse) Homo sapiens mmu05414",2.74440389524853e-08,"16402,12297,12298,16000,210044,16419,21926,12292,11937,11513,326618,11606,22003,12293",5.22816607977513e-08
|
| 181 |
+
"Arachidonic acid metabolism - Mus musculus (house mouse) Homo sapiens mmu00590",3.55488224118131e-08,"17001,12409,13106,11689,67103,54486,21391,15446,18784,19224,64292,18783,13090",6.73452691246016e-08
|
| 182 |
+
"Natural killer cell mediated cytotoxicity - Mus musculus (house mouse) Homo sapiens mmu04650",3.89884559514692e-08,"12506,14939,14102,14127,14972,15040,14964",7.3453389389232e-08
|
| 183 |
+
"Longevity regulating pathway - Mus musculus (house mouse) Homo sapiens mmu04211",4.0771047662804e-08,"11651,11652,20656,16000,210044,18033,108079,18710,207565,16653,13685,11513,16370",7.63897101814074e-08
|
| 184 |
+
"Glioma - Mus musculus (house mouse) Homo sapiens mmu05214",4.17940562551811e-08,"11651,11652,26395,215303,16000,12325,18710,16653,234779,12571,20416,26413",7.78785419836981e-08
|
| 185 |
+
"Fructose and mannose metabolism - Mus musculus (house mouse) Homo sapiens mmu00051",4.61111037237269e-08,"15277,56421,29858,270198,212032,20322,14187,67861,14121",8.54559041836461e-08
|
| 186 |
+
"Adherens junction - Mus musculus (house mouse) Homo sapiens mmu04520",5.33349489589176e-08,"15170,21812,18099,20583,67268,21416,108100,22376,21813,19354,69903,216033,26413",9.8309284297248e-08
|
| 187 |
+
"Viral life cycle - HIV-1 - Mus musculus (house mouse) Homo sapiens mmu03250",5.99114122001517e-08,"17857,192657,80287,218210,17858,101739,69550,319236,209387,667823,12774",1.09837589033611e-07
|
| 188 |
+
"Glycolysis / Gluconeogenesis - Mus musculus (house mouse) Homo sapiens mmu00010",1.16007379910011e-07,"235339,15277,13807,56421,67689,17330,212032,60525,18597,68401,14121",2.11542869247667e-07
|
| 189 |
+
"Hypertrophic cardiomyopathy - Mus musculus (house mouse) Homo sapiens mmu05410",1.4598714851459e-07,"16402,12297,12298,16000,16419,21926,12292,108079,11937,326618,11606,22003,12293",2.64795838529124e-07
|
| 190 |
+
"Bile secretion - Mus musculus (house mouse) Homo sapiens mmu04976",1.64413850764691e-07,"76408,210044,11829,319229,11931,18669,11513,11933,333669,13849,140492,94284,394432",2.96640863019892e-07
|
| 191 |
+
"Cell cycle - Mus musculus (house mouse) Homo sapiens mmu04110",1.77345108184136e-07,"107995,51792,15182,12534,20877,22631,17869,67052,67849,12566,19650,50883,12442,21781,12571,17215",3.18287799425213e-07
|
| 192 |
+
"Salivary secretion - Mus musculus (house mouse) Homo sapiens mmu04970",2.26375637207734e-07,"76113,22318,210044,20496,11931,11550,13010,12494,11513,11933,18796,17105",4.04157551245221e-07
|
| 193 |
+
"Melanoma - Mus musculus (house mouse) Homo sapiens mmu05218",2.48472855210644e-07,"11651,11652,26395,16000,18710,16653,71785,14164,14173,12571,26413",4.41298143889737e-07
|
| 194 |
+
"Other types of O-glycan biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00514",2.83474411632161e-07,"17305,78754,20440,14595,234407,207839,231050,14426,270049",5.00853753194648e-07
|
| 195 |
+
"Cardiac muscle contraction - Mus musculus (house mouse) Homo sapiens mmu04260",2.91782809847246e-07,"12297,12298,12292,11931,11937,12862,326618,22003,11933,12293,236794,12865",5.12875969886139e-07
|
| 196 |
+
"Parkinson disease - Mus musculus (house mouse) Homo sapiens mmu05012",3.16161796589871e-07,"21823,74764,215999,18024,26420,22333,16593,12325,26419,19252,56791,12862,14678,74153,73677,69806,22146,30791,14677,72027,12865",5.5287780839562e-07
|
| 197 |
+
"p53 signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04115",3.80738289784488e-07,"12534,16000,14102,12566,66940,12370,12521,50883,12442,21825,12571",6.59044450845231e-07
|
| 198 |
+
"Gastric acid secretion - Mus musculus (house mouse) Homo sapiens mmu04971",3.80738289784488e-07,"210044,12325,11931,12426,11513,11933,14678,18796,16518,20606,14677",6.59044450845231e-07
|
| 199 |
+
"Phosphatidylinositol signaling system - Mus musculus (house mouse) Homo sapiens mmu04070",6.73160879873606e-07,"53332,72469,271424,74055,18802,16331,18710,74596,327655,234779,320404,18796",1.15933262644899e-06
|
| 200 |
+
"Pancreatic secretion - Mus musculus (house mouse) Homo sapiens mmu04972",7.5547878366619e-07,"210044,20496,319229,11931,12494,12425,11937,11513,11933,22063,18796,18784,233979",1.29456414688528e-06
|
| 201 |
+
"Long-term potentiation - Mus musculus (house mouse) Homo sapiens mmu04720",1.08793555625182e-06,"20111,26395,12325,19057,19055,16653,110651,19058,18796,26413",1.85493012340935e-06
|
| 202 |
+
"Primary bile acid biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00120",1.098877081424e-06,"93732,104086,13123,101502,12642,13124",1.86426410331136e-06
|
| 203 |
+
"Protein processing in endoplasmic reticulum - Mus musculus (house mouse) Homo sapiens mmu04141",1.13008863693484e-06,"18024,140740,26420,20334,15519,26419,67819,57743,12364,69276,67075,56445,12955,108687,17872,216197",1.90772388710288e-06
|
| 204 |
+
"Amyotrophic lateral sclerosis - Mus musculus (house mouse) Homo sapiens mmu05014",1.18813815514367e-06,"74764,215999,19324,22333,16593,218210,19057,67819,21926,12364,19055,21938,21937,12862,19058,432611,73677,226977,105000,75563,22146,19094,11727,12865",1.99583798474873e-06
|
| 205 |
+
"Ferroptosis - Mus musculus (house mouse) Homo sapiens mmu04216",1.59553351211067e-06,"15368,13058,14319,20229,26570,22041,14325,434624",2.6663335773371e-06
|
| 206 |
+
"Aldosterone synthesis and secretion - Mus musculus (house mouse) Homo sapiens mmu04925",1.6029278104226e-06,"215303,210044,12325,12292,11931,18227,11513,11606,11933,14672,18796,16527",2.6663335773371e-06
|
| 207 |
+
"Non-small cell lung cancer - Mus musculus (house mouse) Homo sapiens mmu05223",2.1442335081757e-06,"11651,20848,11652,26395,18710,16653,16453,234779,12571,26413",3.54943507906755e-06
|
| 208 |
+
"PPAR signaling pathway - Mus musculus (house mouse) Homo sapiens mmu03320",2.18574764825953e-06,"66968,16956,93732,104086,13167,11520,12896,108078,109264,11814,13124",3.60067607756764e-06
|
| 209 |
+
"Protein digestion and absorption - Mus musculus (house mouse) Homo sapiens mmu04974",2.39890593046267e-06,"20540,12833,20514,53867,73368,11931,12841,17380,11933,72461,12829,12828",3.93282174176813e-06
|
| 210 |
+
"Endometrial cancer - Mus musculus (house mouse) Homo sapiens mmu05213",2.68269961107506e-06,"11651,11652,26395,17869,21416,18710,16653,216033,26413",4.37703620754353e-06
|
| 211 |
+
"Small cell lung cancer - Mus musculus (house mouse) Homo sapiens mmu05222",3.76450243869314e-06,"11651,11652,17869,14083,12566,18033,18710,11796,12571,12829,12828",6.11283491235411e-06
|
| 212 |
+
"Bacterial invasion of epithelial cells - Mus musculus (house mouse) Homo sapiens mmu05100",3.99899391471502e-06,"16402,234683,66713,14083,15163,18710,11867,20416,216033,56212",6.46282902804655e-06
|
| 213 |
+
"Melanogenesis - Mus musculus (house mouse) Homo sapiens mmu04916",6.90577305836819e-06,"26395,210044,12325,21416,22409,16653,11513,14678,18796,14677,26413",1.11078708155828e-05
|
| 214 |
+
"Pentose and glucuronate interconversions - Mus musculus (house mouse) Homo sapiens mmu00040",8.97431067083743e-06,"110006,20322,14187,67880,94284,67861,394432",1.43673236561294e-05
|
| 215 |
+
"Arrhythmogenic right ventricular cardiomyopathy - Mus musculus (house mouse) Homo sapiens mmu05412",1.09298184576392e-05,"16402,12297,12298,16419,13506,21416,12292,11937,12293,216033",1.74162060469858e-05
|
| 216 |
+
"Amphetamine addiction - Mus musculus (house mouse) Homo sapiens mmu05031",1.16704377828391e-05,"21823,14282,15182,14281,12325,19057,14802,19055,19058",1.85098571346425e-05
|
| 217 |
+
"Folate biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00790",1.18426835460871e-05,"21823,14187,14528,68591,268566,67861",1.86960883759987e-05
|
| 218 |
+
"Arginine and proline metabolism - Mus musculus (house mouse) Homo sapiens mmu00330",1.37261135820985e-05,"20810,18452,66054,67432,20229,242669,18242,66988",2.15696070575833e-05
|
| 219 |
+
"Glycosphingolipid biosynthesis - lacto and neolacto series - Mus musculus (house mouse) Homo sapiens mmu00601",1.49618159788163e-05,"54613,14595,26877,14594,14345,14348",2.34035745356713e-05
|
| 220 |
+
"Cysteine and methionine metabolism - Mus musculus (house mouse) Homo sapiens mmu00270",2.06473558976074e-05,"14711,20810,12411,257635,12035,210808,14204,12116",3.21495358953613e-05
|
| 221 |
+
"Thyroid hormone synthesis - Mus musculus (house mouse) Homo sapiens mmu04918",2.07706010843626e-05,"70337,210044,11931,14725,12640,11513,11933,18796,21819",3.21944316807621e-05
|
| 222 |
+
"Fat digestion and absorption - Mus musculus (house mouse) Homo sapiens mmu04975",2.52367763649752e-05,"11303,237636,19012,110460,67512,18784,50784",3.89400033504821e-05
|
| 223 |
+
"Huntington disease - Mus musculus (house mouse) Homo sapiens mmu05016",2.53822198474667e-05,"74764,20656,15182,26420,22333,16593,26419,14802,12370,12862,432611,73677,226977,18796,105000,75563,22146,12064,12865",3.8988004360298e-05
|
| 224 |
+
"Fatty acid elongation - Mus musculus (house mouse) Homo sapiens mmu00062",2.84765298790708e-05,"54325,54326,74559,66775,83603,70757",4.35448282007315e-05
|
| 225 |
+
"Mucin type O-glycan biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00512",4.19654652451238e-05,"78754,207839,231050,14426,218476,270049",6.38849270026215e-05
|
| 226 |
+
"Steroid biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00100",4.2941009849543e-05,"14137,16889,20652,15490,18194",6.50794860386408e-05
|
| 227 |
+
"Mitophagy - animal - Mus musculus (house mouse) Homo sapiens mmu04137",4.49725193785098e-05,"52440,26420,15251,26419,69104,56715,231874,16653,17684,226421",6.78567659649196e-05
|
| 228 |
+
"Porphyrin metabolism - Mus musculus (house mouse) Homo sapiens mmu00860",4.58662341507329e-05,"15368,14319,110006,14325,94284,434624,394432",6.8900378173568e-05
|
| 229 |
+
"Ovarian steroidogenesis - Mus musculus (house mouse) Homo sapiens mmu04913",4.87350934259658e-05,"16000,210044,11689,15490,12640,11513,18783,16866",7.28888897291858e-05
|
| 230 |
+
"Retinol metabolism - Mus musculus (house mouse) Homo sapiens mmu00830",4.89511446742575e-05,"13087,19682,19892,11668,94284,67442,232174,20148,13090,394432",7.28923158686541e-05
|
| 231 |
+
"Cocaine addiction - Mus musculus (house mouse) Homo sapiens mmu05030",5.27495539392631e-05,"21823,14282,108068,18033,14678,12064,14677",7.82069473621249e-05
|
| 232 |
+
"Biosynthesis of unsaturated fatty acids - Mus musculus (house mouse) Homo sapiens mmu01040",6.0142572383617e-05,"54325,54326,74559,66775,83603,70757",8.83992119948853e-05
|
| 233 |
+
"SNARE interactions in vesicular transport - Mus musculus (house mouse) Homo sapiens mmu04130",6.0142572383617e-05,"22318,58244,20619,20908,22320,53620",8.83992119948853e-05
|
| 234 |
+
"Renal cell carcinoma - Mus musculus (house mouse) Homo sapiens mmu05211",9.32825058288915e-05,"11651,11652,26395,15251,18710,16653,18479,26413",0.000136520748874043
|
| 235 |
+
"Ubiquitin mediated proteolysis - Mus musculus (house mouse) Homo sapiens mmu04120",9.8546765568888e-05,"68612,107995,56791,50754,73998,99375,11796,74153,12703,100763,76980,12702",0.000143156576422935
|
| 236 |
+
"One carbon pool by folate - Mus musculus (house mouse) Homo sapiens mmu00670",9.86562916697645e-05,"14711,17768,216188,12411,22171,12116",0.000143156576422935
|
| 237 |
+
"Cortisol synthesis and secretion - Mus musculus (house mouse) Homo sapiens mmu04927",0.000114082847349455,"210044,12292,11513,11606,14672,18796,16527,18514",0.000164840046382051
|
| 238 |
+
"Aldosterone-regulated sodium reabsorption - Mus musculus (house mouse) Homo sapiens mmu04960",0.000115128213974273,"16000,11931,18710,16653,11933,26413",0.000165648611667625
|
| 239 |
+
"Taste transduction - Mus musculus (house mouse) Homo sapiens mmu04742",0.00011755655242814,"56843,14399,11418,14396,15561,18796,110886,18573,268934",0.000168431867134436
|
| 240 |
+
"Nicotine addiction - Mus musculus (house mouse) Homo sapiens mmu05033",0.000154585803017029,"14399,14802,140919,14396,14402,110886",0.000220559660371577
|
| 241 |
+
"D-Amino acid metabolism - Mus musculus (house mouse) Homo sapiens mmu00470",0.000163608883530001,"217830,14660,216456",0.000232460955348877
|
| 242 |
+
"Histidine metabolism - Mus musculus (house mouse) Homo sapiens mmu00340",0.000164504696045141,"71761,66054,67383,67689,15186",0.000232763906022377
|
| 243 |
+
"Metabolism of xenobiotics by cytochrome P450 - Mus musculus (house mouse) Homo sapiens mmu00980",0.000167237837859422,"67689,12409,13106,54486,13849,13107,94284,394432",0.000235146184515725
|
| 244 |
+
"Spinocerebellar ataxia - Mus musculus (house mouse) Homo sapiens mmu05017",0.000167567515651968,"11651,11652,215999,26420,22333,26419,18044,18710,11937,73677,18796",0.000235146184515725
|
| 245 |
+
"Bladder cancer - Mus musculus (house mouse) Homo sapiens mmu05219",0.00017795827000948,"26395,17869,15200,16653,21825,26413",0.00024870397570997
|
| 246 |
+
"ABC transporters - Mus musculus (house mouse) Homo sapiens mmu02010",0.000180338659063006,"11303,76408,21355,11304,18669,21354,217262",0.000251001970369327
|
| 247 |
+
"Hippo signaling pathway - multiple species - Mus musculus (house mouse) Homo sapiens mmu04392",0.000198491714242032,"18479,213391,232157,319710,22601",0.000274031071079081
|
| 248 |
+
"Folate transport and metabolism - Mus musculus (house mouse) Homo sapiens mmu04981",0.000198491714242032,"76408,22171,101488,14276,12116",0.000274031071079081
|
| 249 |
+
"Protein export - Mus musculus (house mouse) Homo sapiens mmu03060",0.000204033215454344,"140740,57743,69276,24067,100101806,665155",0.000280545671249723
|
| 250 |
+
"Vasopressin-regulated water reabsorption - Mus musculus (house mouse) Homo sapiens mmu04962",0.000265166101378917,"22318,11829,11828,13426,11857,11998",0.000363139118755866
|
| 251 |
+
"Glycerolipid metabolism - Mus musculus (house mouse) Homo sapiens mmu00561",0.000303696192375126,"16956,19012,67512,14187,15450,50784,67861",0.000414241606399672
|
| 252 |
+
"Glycosphingolipid biosynthesis - globo and isoglobo series - Mus musculus (house mouse) Homo sapiens mmu00603",0.000336807359158111,"15212,17939,15211,14348",0.000457574938139107
|
| 253 |
+
"Citrate cycle (TCA cycle) - Mus musculus (house mouse) Homo sapiens mmu00020",0.000454872381101879,"235339,78920,11429,18597,20917",0.000613088861485141
|
| 254 |
+
"Apoptosis - multiple species - Mus musculus (house mouse) Homo sapiens mmu04215",0.000454872381101879,"26420,26419,12370,21937,11796",0.000613088861485141
|
| 255 |
+
"Virion - Hepatitis viruses - Mus musculus (house mouse) Homo sapiens mmu03272",0.000599042725837057,"16784,12512,12527,18417,12520,56173",0.000804226651615892
|
| 256 |
+
"Starch and sucrose metabolism - Mus musculus (house mouse) Homo sapiens mmu00500",0.000696988938794713,"15277,27357,212032,68401,76051",0.000932051875015676
|
| 257 |
+
"Biosynthesis of various nucleotide sugars - Mus musculus (house mouse) Homo sapiens mmu00541",0.000793462605049828,"72017,107652,227620,74091",0.00105280446817895
|
| 258 |
+
"Pantothenate and CoA biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00770",0.000793462605049828,"71743,12035,74450,66812",0.00105280446817895
|
| 259 |
+
"Thyroid cancer - Mus musculus (house mouse) Homo sapiens mmu05216",0.00090477478501694,"26395,17869,21416,16653,26413",0.00119122857795667
|
| 260 |
+
"African trypanosomiasis - Mus musculus (house mouse) Homo sapiens mmu05143",0.00090477478501694,"21926,14102,17874,15894,18796",0.00119122857795667
|
| 261 |
+
"Virion - Herpesvirus - Mus musculus (house mouse) Homo sapiens mmu03266",0.000923082147590435,"16402,231805,545812",0.00121065773972438
|
| 262 |
+
"Proximal tubule bicarbonate reclamation - Mus musculus (house mouse) Homo sapiens mmu04964",0.000954122429343344,"14660,11931,11933,216456",0.0012465737486823
|
| 263 |
+
"Synaptic vesicle cycle - Mus musculus (house mouse) Homo sapiens mmu04721",0.00103077186639531,"27060,11974,22318,242341,140919,12889,20908",0.00134157712381985
|
| 264 |
+
"Mannose type O-glycan biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00515",0.00113634723566088,"14595,243853,14345,14348",0.00146778184606198
|
| 265 |
+
"Terpenoid backbone biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00900",0.00113634723566088,"192156,110460,17855,110196",0.00146778184606198
|
| 266 |
+
"Steroid hormone biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00140",0.00114497178772733,"54200,19682,13106,15490,13123,94284,13090,394432",0.00147334105515101
|
| 267 |
+
"Alanine, aspartate and glutamate metabolism - Mus musculus (house mouse) Homo sapiens mmu00250",0.00115540493066836,"11565,14660,216456,14415,14204",0.00148117699758613
|
| 268 |
+
"Glycine, serine and threonine metabolism - Mus musculus (house mouse) Homo sapiens mmu00260",0.0012983790917614,"14711,71776,12411,257635,12116",0.00165822947674397
|
| 269 |
+
"Notch signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04330",0.00199164747627465,"17305,15182,270118,209200,11491,67122",0.00253414846794648
|
| 270 |
+
"Pyruvate metabolism - Mus musculus (house mouse) Homo sapiens mmu00620",0.00200330075682074,"235339,110460,60525,109264,18597",0.00253950021589544
|
| 271 |
+
"Butanoate metabolism - Mus musculus (house mouse) Homo sapiens mmu00650",0.00211049048567492,"110460,11409,71911,14415",0.00266547131709314
|
| 272 |
+
"Various types of N-glycan biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00513",0.00244494493641174,"15212,15211,14595,67075,330406",0.00305449201419126
|
| 273 |
+
"Valine, leucine and isoleucine biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00290",0.00244538510227042,"257635,12035",0.00305449201419126
|
| 274 |
+
"Virion - Adenovirus - Mus musculus (house mouse) Homo sapiens mmu03267",0.00244538510227042,"13052,12524",0.00305449201419126
|
| 275 |
+
"Propanoate metabolism - Mus musculus (house mouse) Homo sapiens mmu00640",0.00354652753811591,"60525,11409,380660,20917",0.00441374412590338
|
| 276 |
+
"Drug metabolism - other enzymes - Mus musculus (house mouse) Homo sapiens mmu00983",0.00365946996022603,"23917,13106,110006,80914,229363,94284,394432",0.00453774275068028
|
| 277 |
+
"Glutathione metabolism - Mus musculus (house mouse) Homo sapiens mmu00480",0.00387314208278855,"20810,11758,207182,110208,54486,66988",0.00478529510953223
|
| 278 |
+
"beta-Alanine metabolism - Mus musculus (house mouse) Homo sapiens mmu00410",0.00398819256054649,"66054,67689,11409,14415",0.00490965221352474
|
| 279 |
+
"Neomycin, kanamycin and gentamicin biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00524",0.00402025804528273,"15277,212032",0.00493132371741515
|
| 280 |
+
"Tryptophan metabolism - Mus musculus (house mouse) Homo sapiens mmu00380",0.00419179429550433,"107766,78920,110460,70789,14204",0.00512330413894974
|
| 281 |
+
"Glyoxylate and dicarboxylate metabolism - Mus musculus (house mouse) Homo sapiens mmu00630",0.00446558475014848,"11429,110460,67432,60525",0.00543844428500226
|
| 282 |
+
"Nitrogen metabolism - Mus musculus (house mouse) Homo sapiens mmu00910",0.00469988149940458,"56078,12354,23831",0.00570341491564755
|
| 283 |
+
"Pentose phosphate pathway - Mus musculus (house mouse) Homo sapiens mmu00030",0.00497998152391647,"56421,110208,232449,14121",0.00602189255196991
|
| 284 |
+
"mRNA surveillance pathway - Mus musculus (house mouse) Homo sapiens mmu03015",0.00567143961344148,"51792,77305,72930,269643,108062,19826,83410",0.00683378412785705
|
| 285 |
+
"Renin-angiotensin system - Mus musculus (house mouse) Homo sapiens mmu04614",0.00612472396281891,"19025,17380,11606,72461",0.007353981941272
|
| 286 |
+
"Lipoic acid metabolism - Mus musculus (house mouse) Homo sapiens mmu00785",0.00649660836082991,"235339,78920,18597",0.00777313491594035
|
| 287 |
+
"Hedgehog signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04340",0.00668516238827525,"93687,76857,14725,226861,70425",0.00797077053986665
|
| 288 |
+
"Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Mus musculus (house mouse) Homo sapiens mmu00532",0.00865025304510829,"338362,78923,72136",0.0102778267887872
|
| 289 |
+
"Polycomb repressive complex - Mus musculus (house mouse) Homo sapiens mmu03083",0.00953857062383332,"15182,20877,21781,12418,71458,52609",0.0112939325789138
|
| 290 |
+
"Lysine degradation - Mus musculus (house mouse) Homo sapiens mmu00310",0.0100661018991482,"78920,72947,110460,234407,69726",0.0118773036249465
|
| 291 |
+
"Thermogenesis - Mus musculus (house mouse) Homo sapiens mmu04714",0.0106134304361725,"20111,210044,108079,12896,16653,29861,12862,110651,11513,19094,12865",0.0124799302714994
|
| 292 |
+
"Nicotinate and nicotinamide metabolism - Mus musculus (house mouse) Homo sapiens mmu00760",0.0114672455793914,"64383,223646,12494,18950",0.0134375626892525
|
| 293 |
+
"Proteasome - Mus musculus (house mouse) Homo sapiens mmu03050",0.0155468307665519,"19186,16913,73677,16912",0.0180937518477617
|
| 294 |
+
"Base excision repair - Mus musculus (house mouse) Homo sapiens mmu03410",0.0155468307665519,"235587,22256,21665,22594",0.0180937518477617
|
| 295 |
+
"Drug metabolism - cytochrome P450 - Mus musculus (house mouse) Homo sapiens mmu00982",0.0161772199656856,"67689,13106,54486,94284,394432",0.018763374177887
|
| 296 |
+
"Collecting duct acid secretion - Mus musculus (house mouse) Homo sapiens mmu04966",0.0173749611421696,"27060,11974,242341",0.0200842771168808
|
| 297 |
+
"Ascorbate and aldarate metabolism - Mus musculus (house mouse) Homo sapiens mmu00053",0.0273319425829933,"110006,94284,394432",0.0314871365567591
|
| 298 |
+
"RNA degradation - Mus musculus (house mouse) Homo sapiens mmu03018",0.0280038432151324,"13807,56421,210106,214627,240023",0.0321525607284854
|
| 299 |
+
"Valine, leucine and isoleucine degradation - Mus musculus (house mouse) Homo sapiens mmu00280",0.0293698879112335,"110460,11409,12035,14204",0.0336078247574853
|
| 300 |
+
"Circadian rhythm - Mus musculus (house mouse) Homo sapiens mmu04710",0.0320029587058611,"12952,108079,11865",0.0364983575876209
|
| 301 |
+
"Glycosaminoglycan biosynthesis - keratan sulfate - Mus musculus (house mouse) Homo sapiens mmu00533",0.0323807963145611,"76969,14595",0.0368061718108844
|
| 302 |
+
"Endocrine and other factor-regulated calcium reabsorption - Mus musculus (house mouse) Homo sapiens mmu04961",0.0364244805558484,"12062,11931,11933,18796",0.041264943088187
|
| 303 |
+
"Thiamine metabolism - Mus musculus (house mouse) Homo sapiens mmu00730",0.0368636643730356,"11636,78801",0.0416242038119376
|
| 304 |
+
"Chemical carcinogenesis - DNA adducts - Mus musculus (house mouse) Homo sapiens mmu05204",0.0377965526796061,"13106,54486,13849,94284,394432",0.0425367144018009
|
| 305 |
+
"Tyrosine metabolism - Mus musculus (house mouse) Homo sapiens mmu00350",0.0483248120206,"21823,67689,14204",0.0542064503257388
|
| 306 |
+
"ATP-dependent chromatin remodeling - Mus musculus (house mouse) Homo sapiens mmu03082",0.0616447827543476,"56249,15182,404634,29861,93762,269397",0.0689208882597788
|
| 307 |
+
"Arginine biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00220",0.0680505712689631,"14660,216456",0.0753417039049234
|
| 308 |
+
"Phenylalanine metabolism - Mus musculus (house mouse) Homo sapiens mmu00360",0.0680505712689631,"67689,14204",0.0753417039049234
|
| 309 |
+
"Virion - Lassa virus and SFTS virus - Mus musculus (house mouse) Homo sapiens mmu03273",0.0680505712689631,"16784,54216",0.0753417039049234
|
| 310 |
+
"Taurine and hypotaurine metabolism - Mus musculus (house mouse) Homo sapiens mmu00430",0.0738690852395206,"207182,14415",0.0815189581445843
|
| 311 |
+
"Glycosaminoglycan biosynthesis - heparan sulfate / heparin - Mus musculus (house mouse) Homo sapiens mmu00534",0.0859545552860372,"195646,50786",0.0945500108146409
|
| 312 |
+
"Fatty acid degradation - Mus musculus (house mouse) Homo sapiens mmu00071",0.0905913527719386,"110460,12896,11409",0.0993300684734117
|
| 313 |
+
"alpha-Linolenic acid metabolism - Mus musculus (house mouse) Homo sapiens mmu00592",0.0922044611045341,"18784,18783",0.100774747553353
|
| 314 |
+
"Linoleic acid metabolism - Mus musculus (house mouse) Homo sapiens mmu00591",0.102938306539596,"13106,18784,18783",0.112146845143777
|
| 315 |
+
"Peroxisome - Mus musculus (house mouse) Homo sapiens mmu04146",0.103588311414573,"20656,93732,56794,17855",0.112495586599903
|
| 316 |
+
"Phototransduction - Mus musculus (house mouse) Homo sapiens mmu04744",0.105078120804701,"14913,14688",0.113391263273427
|
| 317 |
+
"Maturity onset diabetes of the young - Mus musculus (house mouse) Homo sapiens mmu04950",0.105078120804701,"15242,18012",0.113391263273427
|
| 318 |
+
"Pyrimidine metabolism - Mus musculus (house mouse) Homo sapiens mmu00240",0.11151813771352,"22171,80914,12495",0.119583914969529
|
| 319 |
+
"N-Glycan biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00510",0.11151813771352,"20440,14595,67075",0.119583914969529
|
| 320 |
+
"Phosphonate and phosphinate metabolism - Mus musculus (house mouse) Homo sapiens mmu00440",0.116713829983505,"68671",0.12476305963754
|
| 321 |
+
"Oxidative phosphorylation - Mus musculus (house mouse) Homo sapiens mmu00190",0.164047288933555,"27060,11974,242341,12862,12865",0.17481289226982
|
| 322 |
+
"DNA replication - Mus musculus (house mouse) Homo sapiens mmu03030",0.167755375552114,"327762,17215",0.178207423873118
|
| 323 |
+
"Phenylalanine, tyrosine and tryptophan biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00400",0.169860547634496,"14204",0.179883374979388
|
| 324 |
+
"Virion - Human immunodeficiency virus - Mus musculus (house mouse) Homo sapiens mmu03260",0.186856052659539,"12774",0.197269083457903
|
| 325 |
+
"Sulfur metabolism - Mus musculus (house mouse) Homo sapiens mmu00920",0.203503755797242,"59010",0.21418142199648
|
| 326 |
+
"Ubiquinone and other terpenoid-quinone biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00130",0.219810771550366,"27973",0.230632224919
|
| 327 |
+
"Fanconi anemia pathway - Mus musculus (house mouse) Homo sapiens mmu03460",0.288196393506123,"74386,208836",0.301456963759472
|
| 328 |
+
"Virion - Ebolavirus, Lyssavirus and Morbillivirus - Mus musculus (house mouse) Homo sapiens mmu03265",0.296474529085686,"14130",0.308225043957985
|
| 329 |
+
"Cobalamin transport and metabolism - Mus musculus (house mouse) Homo sapiens mmu04980",0.296474529085686,"21452",0.308225043957985
|
| 330 |
+
"Basal cell carcinoma - Mus musculus (house mouse) Homo sapiens mmu05217",0.370609503688799,"21416,22409",0.384127175555867
|
| 331 |
+
"Mismatch repair - Mus musculus (house mouse) Homo sapiens mmu03430",0.378597484291773,"17685",0.391217400434832
|
| 332 |
+
"Vitamin digestion and absorption - Mus musculus (house mouse) Homo sapiens mmu04977",0.415992390459541,"21452",0.428560136394875
|
| 333 |
+
"Glycosylphosphatidylinositol (GPI)-anchor biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00563",0.462376754196789,"70325",0.474911063798509
|
| 334 |
+
"RNA polymerase - Mus musculus (house mouse) Homo sapiens mmu03020",0.484169141410898,"70408",0.494316398865617
|
| 335 |
+
"Autophagy - other - Mus musculus (house mouse) Homo sapiens mmu04136",0.484169141410898,"242557",0.494316398865617
|
| 336 |
+
"Basal transcription factors - Mus musculus (house mouse) Homo sapiens mmu03022",0.597583102386211,"319944",0.608286083324472
|
| 337 |
+
"Nucleocytoplasmic transport - Mus musculus (house mouse) Homo sapiens mmu03013",0.698260660880753,"218210,19826",0.707091870089714
|
| 338 |
+
"Nucleotide excision repair - Mus musculus (house mouse) Homo sapiens mmu03420",0.698797537302738,"99375",0.707091870089714
|
| 339 |
+
"Ribosome biogenesis in eukaryotes - Mus musculus (house mouse) Homo sapiens mmu03008",0.822934521827145,"237107,27993",0.830238674387741
|
| 340 |
+
"Ribosome - Mus musculus (house mouse) Homo sapiens mmu03010",0.904755003240845,"77721,68172,100042335,108168333",0.910092790870585
|
| 341 |
+
"Spliceosome - Mus musculus (house mouse) Homo sapiens mmu03040",0.999982533755008,"66492,57317,13204,54633,67229,108121",0.999999783530653
|
| 342 |
+
"Olfactory transduction - Mus musculus (house mouse) Homo sapiens mmu04740",0.999999783530653,"12325,14688,18573,545205,258325",0.999999783530653
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/kegg_enrichment.R
ADDED
|
@@ -0,0 +1,115 @@
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
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|
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|
|
|
|
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|
|
|
|
|
|
|
|
|
| 1 |
+
|
| 2 |
+
# Load required libraries
|
| 3 |
+
library(org.Mm.eg.db)
|
| 4 |
+
library(KEGGREST)
|
| 5 |
+
|
| 6 |
+
# Function to get KEGG pathway enrichment
|
| 7 |
+
enrich_kegg_custom <- function(gene_ids, organism = "mmu", pvalue_cutoff = 0.05) {
|
| 8 |
+
# Convert Ensembl IDs to Entrez IDs
|
| 9 |
+
entrez_ids <- mapIds(org.Mm.eg.db, keys = gene_ids, column = "ENTREZID", keytype = "ENSEMBL", multiVals = "first")
|
| 10 |
+
entrez_ids <- entrez_ids[!is.na(entrez_ids)]
|
| 11 |
+
|
| 12 |
+
if (length(entrez_ids) < 2) {
|
| 13 |
+
return(data.frame())
|
| 14 |
+
}
|
| 15 |
+
|
| 16 |
+
# Get all KEGG pathways for the organism
|
| 17 |
+
pathways <- keggList("pathway", organism)
|
| 18 |
+
pathway_ids <- names(pathways)
|
| 19 |
+
|
| 20 |
+
# Get all mouse genes in KEGG (for background)
|
| 21 |
+
all_entrez <- keys(org.Mm.eg.db, keytype = "ENTREZID")
|
| 22 |
+
bg_genes <- length(all_entrez)
|
| 23 |
+
|
| 24 |
+
results <- data.frame()
|
| 25 |
+
|
| 26 |
+
for (pid in pathway_ids) {
|
| 27 |
+
# Get genes in this pathway
|
| 28 |
+
pathway_name <- pathways[pid]
|
| 29 |
+
# Extract clean pathway name - remove leading number and space
|
| 30 |
+
pathway_clean <- sub("^[0-9]+ +", "", pathway_name)
|
| 31 |
+
|
| 32 |
+
tryCatch({
|
| 33 |
+
pathway_info <- keggGet(pid)
|
| 34 |
+
pathway_genes <- pathway_info[[1]]$GENE
|
| 35 |
+
if (is.null(pathway_genes)) next
|
| 36 |
+
|
| 37 |
+
# KEGG returns genes as alternating id and description
|
| 38 |
+
pathway_entrez <- pathway_genes[seq(1, length(pathway_genes), 2)]
|
| 39 |
+
|
| 40 |
+
# Remove any non-numeric entries
|
| 41 |
+
pathway_entrez <- pathway_entrez[grepl("^[0-9]+$", pathway_entrez)]
|
| 42 |
+
|
| 43 |
+
if (length(pathway_entrez) < 1) next
|
| 44 |
+
|
| 45 |
+
# Calculate overlap
|
| 46 |
+
sig_entrez_unique <- unique(as.character(na.omit(entrez_ids)))
|
| 47 |
+
pathway_entrez_unique <- unique(pathway_entrez)
|
| 48 |
+
|
| 49 |
+
overlap <- intersect(sig_entrez_unique, pathway_entrez_unique)
|
| 50 |
+
gene_in_pathway <- length(overlap)
|
| 51 |
+
|
| 52 |
+
if (gene_in_pathway < 1) next
|
| 53 |
+
|
| 54 |
+
# Hypergeometric test
|
| 55 |
+
m <- length(pathway_entrez_unique)
|
| 56 |
+
n <- bg_genes - m
|
| 57 |
+
k <- length(sig_entrez_unique)
|
| 58 |
+
|
| 59 |
+
pval <- phyper(gene_in_pathway - 1, m, n, k, lower.tail = FALSE)
|
| 60 |
+
|
| 61 |
+
results <- rbind(results, data.frame(
|
| 62 |
+
pathway = paste0(pathway_clean, " Homo sapiens ", pid),
|
| 63 |
+
pvalue = pval,
|
| 64 |
+
overlap_genes = paste(overlap, collapse = ","),
|
| 65 |
+
stringsAsFactors = FALSE
|
| 66 |
+
))
|
| 67 |
+
}, error = function(e) {
|
| 68 |
+
# Skip if error
|
| 69 |
+
})
|
| 70 |
+
}
|
| 71 |
+
|
| 72 |
+
# Adjust p-values
|
| 73 |
+
if (nrow(results) > 0) {
|
| 74 |
+
results$padj <- p.adjust(results$pvalue, method = "BH")
|
| 75 |
+
results <- results[order(results$pvalue), ]
|
| 76 |
+
}
|
| 77 |
+
|
| 78 |
+
return(results)
|
| 79 |
+
}
|
| 80 |
+
|
| 81 |
+
# Load significant gene lists
|
| 82 |
+
cat("Loading gene lists...\n")
|
| 83 |
+
|
| 84 |
+
# 5xFAD
|
| 85 |
+
sig_5xfad <- read.table("/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/sig_genes_5xfad.txt", header = FALSE, stringsAsFactors = FALSE)
|
| 86 |
+
genes_5xfad <- sig_5xfad$V1
|
| 87 |
+
cat("5xFAD significant genes:", length(genes_5xfad), "\n")
|
| 88 |
+
|
| 89 |
+
# 3xTg-AD
|
| 90 |
+
sig_3xtg <- read.table("/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/sig_genes_3xtg.txt", header = FALSE, stringsAsFactors = FALSE)
|
| 91 |
+
genes_3xtg <- sig_3xtg$V1
|
| 92 |
+
cat("3xTg-AD significant genes:", length(genes_3xtg), "\n")
|
| 93 |
+
|
| 94 |
+
# PS3O1S
|
| 95 |
+
sig_ps3 <- read.table("/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/sig_genes_ps3o1s.txt", header = FALSE, stringsAsFactors = FALSE)
|
| 96 |
+
genes_ps3 <- sig_ps3$V1
|
| 97 |
+
cat("PS3O1S significant genes:", length(genes_ps3), "\n")
|
| 98 |
+
|
| 99 |
+
# Run KEGG enrichment for each model
|
| 100 |
+
cat("\nRunning KEGG enrichment for 5xFAD...\n")
|
| 101 |
+
kegg_5xfad <- enrich_kegg_custom(genes_5xfad)
|
| 102 |
+
write.csv(kegg_5xfad, "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/kegg_5xfad.csv", row.names = FALSE)
|
| 103 |
+
cat("5xFAD enriched pathways:", nrow(kegg_5xfad), "\n")
|
| 104 |
+
|
| 105 |
+
cat("\nRunning KEGG enrichment for 3xTg-AD...\n")
|
| 106 |
+
kegg_3xtg <- enrich_kegg_custom(genes_3xtg)
|
| 107 |
+
write.csv(kegg_3xtg, "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/kegg_3xtg.csv", row.names = FALSE)
|
| 108 |
+
cat("3xTg-AD enriched pathways:", nrow(kegg_3xtg), "\n")
|
| 109 |
+
|
| 110 |
+
cat("\nRunning KEGG enrichment for PS3O1S...\n")
|
| 111 |
+
kegg_ps3 <- enrich_kegg_custom(genes_ps3)
|
| 112 |
+
write.csv(kegg_ps3, "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/kegg_ps3o1s.csv", row.names = FALSE)
|
| 113 |
+
cat("PS3O1S enriched pathways:", nrow(kegg_ps3), "\n")
|
| 114 |
+
|
| 115 |
+
cat("\nDone!\n")
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/kegg_ps3o1s.csv
ADDED
|
@@ -0,0 +1,294 @@
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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| 1 |
+
"pathway","pvalue","overlap_genes","padj"
|
| 2 |
+
"Neuroactive ligand signaling - Mus musculus (house mouse) Homo sapiens mmu04082",9.81107023474811e-12,"14395,20511,20513,11540,104111,15550,18387,70155,14681,11551,14701,13492,242443,15551",2.8746435787812e-09
|
| 3 |
+
"Lysosome biogenesis - Mus musculus (house mouse) Homo sapiens mmu04142",3.06384304474036e-10,"14667,27060,11772,11767,19156,12514,66049,63959,71718,74245,52187,71665,74105,240283",4.48853006054463e-08
|
| 4 |
+
"Protein processing in endoplasmic reticulum - Mus musculus (house mouse) Homo sapiens mmu04141",8.39651727606864e-09,"71853,12033,59007,67819,18415,14828,386649,67437,12282,223455,75744",8.20059853962703e-07
|
| 5 |
+
"Hormone signaling - Mus musculus (house mouse) Homo sapiens mmu04081",6.60387911884491e-08,"12921,104111,18387,53945,14681,11551,20605,14701,13492,56508,12167",4.8373414545539e-06
|
| 6 |
+
"Cadherin signaling - Mus musculus (house mouse) Homo sapiens mmu04519",1.45175636008651e-07,"14395,59287,216965,54401,353499,29806,208846,57265,93880,242894,14107,93700,192164,93712",8.50729227010695e-06
|
| 7 |
+
"Hippo signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04390",3.46751452535817e-07,"21803,56513,54401,13385,13383,12234,29806,57265,12167",1.62846310542203e-05
|
| 8 |
+
"Glutamatergic synapse - Mus musculus (house mouse) Homo sapiens mmu04724",3.89052619042805e-07,"20511,20513,104111,13385,18805,14681,14701,242443",1.62846310542203e-05
|
| 9 |
+
"Neuroactive ligand-receptor interaction - Mus musculus (house mouse) Homo sapiens mmu04080",5.15672881349604e-07,"14395,12921,11540,15550,18387,70155,11551,20605,19773,13492,242443,12257,15551",1.88865192794293e-05
|
| 10 |
+
"cAMP signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04024",7.36310490653198e-07,"12921,11540,104111,15550,18805,20605,13492,242443,56508,15551",2.39709970845986e-05
|
| 11 |
+
"Human papillomavirus infection - Mus musculus (house mouse) Homo sapiens mmu05165",1.1905573282264e-06,"27060,56513,16773,13383,19106,20750,19303,19651,15015,235542,57265,21770",3.48833297170336e-05
|
| 12 |
+
"Chemokine signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04062",1.9208159563733e-06,"20302,14773,18803,104111,20300,56744,19303,18036,14701",5.11635522924889e-05
|
| 13 |
+
"Other types of O-glycan biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00514",5.69086529972916e-06,"108760,53418,224143,108155,381694",0.000138951961068387
|
| 14 |
+
"IgSF CAM signaling - Mus musculus (house mouse) Homo sapiens mmu04517",9.84253307353294e-06,"56513,56455,18803,218397,13449,108100,19303,241568,242894,11735",0.000212815162957305
|
| 15 |
+
"Axon guidance - Mus musculus (house mouse) Homo sapiens mmu04360",1.01686425986426e-05,"56513,18803,16886,218397,245857,241568,12167,235611",0.000212815162957305
|
| 16 |
+
"Human immunodeficiency virus 1 infection - Mus musculus (house mouse) Homo sapiens mmu05170",1.11221744409193e-05,"11767,18803,16886,21356,12234,19303,14681,15015,14701",0.000214591386803515
|
| 17 |
+
"Fanconi anemia pathway - Mus musculus (house mouse) Homo sapiens mmu03460",1.17183009858575e-05,"67030,71718,60534,108167613,18861",0.000214591386803515
|
| 18 |
+
"Morphine addiction - Mus musculus (house mouse) Homo sapiens mmu05032",1.57924334204489e-05,"14395,14773,104111,218461,14681,14701",0.000272187234834795
|
| 19 |
+
"Fc gamma R-mediated phagosome formation - Mus musculus (house mouse) Homo sapiens mmu04666",1.67891012402318e-05,"18803,16886,18805,16332,53357,242894",0.000273289259077107
|
| 20 |
+
"Pathways of neurodegeneration - multiple diseases - Mus musculus (house mouse) Homo sapiens mmu05022",2.38706044331941e-05,"18803,13385,67819,23997,12869,14828,17992,73916,66725,230908,217695,57265",0.000368109847311888
|
| 21 |
+
"Endocytosis - Mus musculus (house mouse) Homo sapiens mmu04144",2.56928028938638e-05,"11772,14773,56513,18805,27965,15015,347722,242894,259300",0.000368299021847458
|
| 22 |
+
"Glycerophospholipid metabolism - Mus musculus (house mouse) Homo sapiens mmu00564",2.67290030027644e-05,"12651,18805,75320,233552,241274,53357",0.000368299021847458
|
| 23 |
+
"Alcoholism - Mus musculus (house mouse) Homo sapiens mmu05034",2.7653851469775e-05,"11540,63959,14681,14701,242443,319177,319183,97114",0.000368299021847458
|
| 24 |
+
"Ubiquitin mediated proteolysis - Mus musculus (house mouse) Homo sapiens mmu04120",3.30644983292565e-05,"67030,68729,12234,66799,69807,140630,433742",0.000421212956977051
|
| 25 |
+
"Efferocytosis - Mus musculus (house mouse) Homo sapiens mmu04148",4.37203242840502e-05,"21803,20393,50769,12894,53357,497097,11491",0.000533752292301112
|
| 26 |
+
"Viral carcinogenesis - Mus musculus (house mouse) Homo sapiens mmu05203",4.97257421258577e-05,"54401,13383,19106,19303,19651,15015,319177,319183",0.000582785697715053
|
| 27 |
+
"Regulation of actin cytoskeleton - Mus musculus (house mouse) Homo sapiens mmu04810",6.34326748019767e-05,"16886,13367,108100,19303,245857,14701,242894,17451",0.000714837450653045
|
| 28 |
+
"Selenocompound metabolism - Mus musculus (house mouse) Homo sapiens mmu00450",0.000114410026166458,"50493,70266,214580",0.0012415606543249
|
| 29 |
+
"Base excision repair - Mus musculus (house mouse) Homo sapiens mmu03410",0.000147378833822597,"235587,100206,328417,16881",0.00154221422535789
|
| 30 |
+
"Proteoglycans in cancer - Mus musculus (house mouse) Homo sapiens mmu05205",0.000177162329137342,"21803,18803,15163,19303,17022,57265,11735",0.00178995042887038
|
| 31 |
+
"Taste transduction - Mus musculus (house mouse) Homo sapiens mmu04742",0.000184227451937188,"14395,15550,15551,574417,20269",0.00179928811391987
|
| 32 |
+
"Rap1 signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04015",0.000237179245694347,"56513,18803,11540,104111,74206,14681,56508",0.00224172641898205
|
| 33 |
+
"Hypertrophic cardiomyopathy - Mus musculus (house mouse) Homo sapiens mmu05410",0.000271814518334427,"21803,16773,11421,19079,140723",0.0024888016834996
|
| 34 |
+
"Mismatch repair - Mus musculus (house mouse) Homo sapiens mmu03430",0.000290557706925856,"108167613,16881,18861",0.00257980024634169
|
| 35 |
+
"Chagas disease - Mus musculus (house mouse) Homo sapiens mmu05142",0.000311710520596121,"20302,21803,11421,16159,14681",0.00265284363552
|
| 36 |
+
"Amyotrophic lateral sclerosis - Mus musculus (house mouse) Homo sapiens mmu05014",0.00031765193361002,"227720,20511,11744,67819,23997,12869,14828,17992,230908",0.00265284363552
|
| 37 |
+
"mRNA surveillance pathway - Mus musculus (house mouse) Homo sapiens mmu03015",0.000325946658289147,"56422,66899,230908,235542,21770",0.00265284363552
|
| 38 |
+
"Pathways in cancer - Mus musculus (house mouse) Homo sapiens mmu05200",0.000343836184543039,"21803,18803,22032,16773,50493,104111,18805,16159,14701,19401,57265",0.00272281086678677
|
| 39 |
+
"Toxoplasmosis - Mus musculus (house mouse) Homo sapiens mmu05145",0.000404643454268753,"21803,16773,16159,18036,14681",0.00308066123351916
|
| 40 |
+
"Huntington disease - Mus musculus (house mouse) Homo sapiens mmu05016",0.000410053884325076,"11772,20511,13385,23997,12869,231329,17992,73916",0.00308066123351916
|
| 41 |
+
"Tight junction - Mus musculus (house mouse) Homo sapiens mmu04530",0.000427474069909468,"56513,15525,13383,15163,19079,242894",0.00313124756208685
|
| 42 |
+
"Thermogenesis - Mus musculus (house mouse) Homo sapiens mmu04714",0.000449245147413152,"52469,104111,12894,12869,83379,19079,17992",0.00321045922419643
|
| 43 |
+
"Parathyroid hormone synthesis, secretion and action - Mus musculus (house mouse) Homo sapiens mmu04928",0.000537894270335414,"20393,104111,53416,18805,23948",0.00375245288591134
|
| 44 |
+
"Cellular senescence - Mus musculus (house mouse) Homo sapiens mmu04218",0.000613316457287935,"21803,15257,103213,12234,19651,15015",0.00417910981361314
|
| 45 |
+
"Human cytomegalovirus infection - Mus musculus (house mouse) Homo sapiens mmu05163",0.000659759566751578,"20302,104111,21356,19303,14681,15015,14701",0.00435638385800762
|
| 46 |
+
"T cell receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04660",0.000676243866509804,"18803,13383,18036,235542,21770",0.00435638385800762
|
| 47 |
+
"Leishmaniasis - Mus musculus (house mouse) Homo sapiens mmu05140",0.000683937397502903,"21803,12946,16159,18036",0.00435638385800762
|
| 48 |
+
"Oocyte meiosis - Mus musculus (house mouse) Homo sapiens mmu04114",0.000701663380654805,"54401,104111,12234,21770,17451",0.00437419937301825
|
| 49 |
+
"Relaxin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04926",0.00093153188399305,"21803,104111,14681,14701,19773",0.00568622587520758
|
| 50 |
+
"Synaptic vesicle cycle - Mus musculus (house mouse) Homo sapiens mmu04721",0.000978589078033985,"27060,11772,20511,20513",0.00585156326252975
|
| 51 |
+
"Parkinson disease - Mus musculus (house mouse) Homo sapiens mmu05012",0.00102528873671163,"18803,11540,23997,12869,14828,17992,66725",0.00600819199713013
|
| 52 |
+
"Dopaminergic synapse - Mus musculus (house mouse) Homo sapiens mmu04728",0.00113753203036611,"14681,14701,13492,235542,21770",0.00640955547879367
|
| 53 |
+
"Serotonergic synapse - Mus musculus (house mouse) Homo sapiens mmu04726",0.00113753203036611,"15550,14681,14701,15551,56448",0.00640955547879367
|
| 54 |
+
"Apelin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04371",0.00125232324673642,"104111,20750,19079,18791,14701",0.00688148819400325
|
| 55 |
+
"Neutrophil extracellular trap formation - Mus musculus (house mouse) Homo sapiens mmu04613",0.0012887413045722,"12727,12946,18803,319177,319183,97114",0.00688148819400325
|
| 56 |
+
"PI3K-Akt signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04151",0.00129174693061495,"54401,16773,20393,20750,19651,14701,235542,21770",0.00688148819400325
|
| 57 |
+
"Antigen processing and presentation - Mus musculus (house mouse) Homo sapiens mmu04612",0.00147560659700572,"15525,21356,14828,15015",0.00772058451647636
|
| 58 |
+
"Diabetic cardiomyopathy - Mus musculus (house mouse) Homo sapiens mmu05415",0.00152320077995881,"21803,11421,12869,17992,14583,14782",0.00782978646540231
|
| 59 |
+
"Lipid and atherosclerosis - Mus musculus (house mouse) Homo sapiens mmu05417",0.00155917620292144,"20302,16803,18803,15525,14828,16159",0.00787652805958587
|
| 60 |
+
"Polycomb repressive complex - Mus musculus (house mouse) Homo sapiens mmu03083",0.0016061025990886,"22658,22632,108155,12418",0.00797606883954168
|
| 61 |
+
"PPAR signaling pathway - Mus musculus (house mouse) Homo sapiens mmu03320",0.00167426429745366,"57875,56473,12894,104086",0.00817599065256539
|
| 62 |
+
"Protein export - Mus musculus (house mouse) Homo sapiens mmu03060",0.00173952519554255,"71446,224727,14828",0.0083554242999011
|
| 63 |
+
"GABAergic synapse - Mus musculus (house mouse) Homo sapiens mmu04727",0.00181656385088605,"14395,104111,14681,14701",0.00858315251915506
|
| 64 |
+
"Integrin signaling - Mus musculus (house mouse) Homo sapiens mmu04518",0.00185074524827744,"21803,16773,108101,20750,19303",0.00858315251915506
|
| 65 |
+
"Oxytocin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04921",0.00190411233360095,"104111,19079,14681,140723,16520",0.00858315251915506
|
| 66 |
+
"Retrograde endocannabinoid signaling - Mus musculus (house mouse) Homo sapiens mmu04723",0.00190411233360095,"14395,104111,17992,14681,14701",0.00858315251915506
|
| 67 |
+
"Adrenergic signaling in cardiomyocytes - Mus musculus (house mouse) Homo sapiens mmu04261",0.00201420881806829,"104111,140723,235542,56508,21770",0.00882644990287597
|
| 68 |
+
"Ubiquinone and other terpenoid-quinone biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00130",0.0020183349607259,"230027,71883",0.00882644990287597
|
| 69 |
+
"Cell cycle - Mus musculus (house mouse) Homo sapiens mmu04110",0.00207096578561056,"21803,54401,26429,19651,21770",0.00892342610564549
|
| 70 |
+
"Cushing syndrome - Mus musculus (house mouse) Homo sapiens mmu04934",0.00237239082116221,"12921,104111,218461,58226,57265",0.0100740653710222
|
| 71 |
+
"Circadian entrainment - Mus musculus (house mouse) Homo sapiens mmu04713",0.00256134584997573,"104111,58226,14681,14701",0.0107210619148984
|
| 72 |
+
"Autophagy - animal - Mus musculus (house mouse) Homo sapiens mmu04140",0.00270448733141765,"52187,78610,217695,50540,73683",0.0111607716634559
|
| 73 |
+
"Dilated cardiomyopathy - Mus musculus (house mouse) Homo sapiens mmu05414",0.00285002066115343,"21803,16773,104111,140723",0.0115980007460827
|
| 74 |
+
"Toll-like receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04620",0.002950983621268,"20302,16803,16159,20750",0.0118443589182401
|
| 75 |
+
"Cholesterol metabolism - Mus musculus (house mouse) Homo sapiens mmu04979",0.00303938443540925,"57875,104086,12257",0.0119323757949965
|
| 76 |
+
"Th17 cell differentiation - Mus musculus (house mouse) Homo sapiens mmu04659",0.00305436240486259,"21803,18803,18036,19401",0.0119323757949965
|
| 77 |
+
"Coronavirus disease - Mus musculus (house mouse) Homo sapiens mmu05171",0.00312238417828651,"18803,11421,19106,16159,18036,11491,108168832",0.0120376126873414
|
| 78 |
+
"Calcium signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04020",0.00347224424994416,"18803,11540,104111,58226,13492,242443",0.0132125657822551
|
| 79 |
+
"Insulin resistance - Mus musculus (house mouse) Homo sapiens mmu04931",0.0036084634732197,"12894,19079,14583,108155",0.0135548692006843
|
| 80 |
+
"Tuberculosis - Mus musculus (house mouse) Homo sapiens mmu05152",0.00372395064813506,"27060,21803,16803,12946,16159",0.0138116144291592
|
| 81 |
+
"Cholinergic synapse - Mus musculus (house mouse) Homo sapiens mmu04725",0.00409802877013997,"104111,14681,14701,16520",0.0150090303706376
|
| 82 |
+
"Nucleotide excision repair - Mus musculus (house mouse) Homo sapiens mmu03420",0.00437422571366551,"231329,108167613,16881",0.0158228164704197
|
| 83 |
+
"Legionellosis - Mus musculus (house mouse) Homo sapiens mmu05134",0.00458946133633355,"12946,56422,16159",0.0163989289212894
|
| 84 |
+
"Prion disease - Mus musculus (house mouse) Homo sapiens mmu05020",0.00482564340860616,"20867,23997,12869,14828,17992,242443",0.0170351026352001
|
| 85 |
+
"AMPK signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04152",0.00599451995233028,"12894,19079,235542,21770",0.0207979219693438
|
| 86 |
+
"Focal adhesion - Mus musculus (house mouse) Homo sapiens mmu04510",0.00603352685117482,"16773,13731,13367,20750,19303",0.0207979219693438
|
| 87 |
+
"Biosynthesis of various nucleotide sugars - Mus musculus (house mouse) Homo sapiens mmu00541",0.00620996651537523,"109754,76355",0.0211340730328161
|
| 88 |
+
"Malaria - Mus musculus (house mouse) Homo sapiens mmu05144",0.00627530496196246,"21803,12946,16159",0.0211340730328161
|
| 89 |
+
"Sphingolipid signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04071",0.00667797559028275,"66844,18805,235542,21770",0.0222346232721914
|
| 90 |
+
"Cytokine-cytokine receptor interaction - Mus musculus (house mouse) Homo sapiens mmu04060",0.0068534953991665,"20302,21803,20300,16159,56744,12167",0.0225626309208515
|
| 91 |
+
"FoxO signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04068",0.00703824121203174,"21803,20393,19079,19651",0.0227119998276805
|
| 92 |
+
"Alzheimer disease - Mus musculus (house mouse) Homo sapiens mmu05010",0.00705389755740247,"59287,19106,23997,12869,17992,57265,11491",0.0227119998276805
|
| 93 |
+
"MAPK signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04010",0.00741537655421076,"21803,216965,218397,58226,14701,140723",0.0233961142953645
|
| 94 |
+
"Mannose type O-glycan biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00515",0.00742607040774367,"53418,74653",0.0233961142953645
|
| 95 |
+
"Yersinia infection - Mus musculus (house mouse) Homo sapiens mmu05135",0.00760232082148642,"18803,108100,19303,242894",0.02369659575208
|
| 96 |
+
"Adipocytokine signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04920",0.00797809815764336,"12894,19079,18036",0.0243498204186407
|
| 97 |
+
"Cortisol synthesis and secretion - Mus musculus (house mouse) Homo sapiens mmu04927",0.00797809815764336,"104111,218461,58226",0.0243498204186407
|
| 98 |
+
"Transcriptional misregulation in cancer - Mus musculus (house mouse) Homo sapiens mmu05202",0.00839886129866956,"18124,17355,18791,19401,97114",0.0253697562939194
|
| 99 |
+
"Thyroid hormone synthesis - Mus musculus (house mouse) Homo sapiens mmu04918",0.00860015296986339,"104111,14828,14782",0.025473415103247
|
| 100 |
+
"Alcoholic liver disease - Mus musculus (house mouse) Homo sapiens mmu04936",0.0086070583454657,"16803,12894,16159,19079",0.025473415103247
|
| 101 |
+
"alpha-Linolenic acid metabolism - Mus musculus (house mouse) Homo sapiens mmu00592",0.00874040284972734,"56473,53357",0.0256093803497011
|
| 102 |
+
"Bacterial invasion of epithelial cells - Mus musculus (house mouse) Homo sapiens mmu05100",0.00958521023699727,"15163,19303,242894",0.0278065999944574
|
| 103 |
+
"Epstein-Barr virus infection - Mus musculus (house mouse) Homo sapiens mmu05169",0.00970735538352041,"19106,21356,23997,18036,15015",0.0278848541899165
|
| 104 |
+
"Chemical carcinogenesis - reactive oxygen species - Mus musculus (house mouse) Homo sapiens mmu05208",0.0100551237613953,"171429,12869,18805,17992,11431",0.0285973853495971
|
| 105 |
+
"Glycosphingolipid biosynthesis - lacto and neolacto series - Mus musculus (house mouse) Homo sapiens mmu00601",0.0101506077691403,"53418,93961",0.0285973853495971
|
| 106 |
+
"Phospholipase D signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04072",0.0103883732407557,"18803,104111,18805,56508",0.0289885081861089
|
| 107 |
+
"Systemic lupus erythematosus - Mus musculus (house mouse) Homo sapiens mmu05322",0.010626487476031,"20821,319177,319183,97114",0.0293732153818592
|
| 108 |
+
"Cytosolic DNA-sensing pathway - Mus musculus (house mouse) Homo sapiens mmu04623",0.0113674752838335,"72935,18036,22040",0.0311277594220861
|
| 109 |
+
"Ras signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04014",0.0115315930608717,"18803,218397,18805,14701,53357",0.0312847848781055
|
| 110 |
+
"Glycosylphosphatidylinositol (GPI)-anchor biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00563",0.0124406214665916,"110417,233575",0.0334413035753334
|
| 111 |
+
"mTOR signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04150",0.0126587609908749,"20393,71718,52187,57265",0.033718336093876
|
| 112 |
+
"Human T-cell leukemia virus 1 infection - Mus musculus (house mouse) Homo sapiens mmu05166",0.0131490284129182,"21803,104111,13383,15015,12257",0.0347086966214868
|
| 113 |
+
"Rheumatoid arthritis - Mus musculus (house mouse) Homo sapiens mmu05323",0.0133279844533338,"20302,27060,21803",0.0348669593288109
|
| 114 |
+
"Th1 and Th2 cell differentiation - Mus musculus (house mouse) Homo sapiens mmu04658",0.0137416979305425,"18803,16159,18036",0.0353696925773881
|
| 115 |
+
"Non-alcoholic fatty liver disease - Mus musculus (house mouse) Homo sapiens mmu04932",0.0137615868731135,"21803,12869,19079,17992",0.0353696925773881
|
| 116 |
+
"Mucin type O-glycan biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00512",0.0140804635503338,"108760,218476",0.0358745723499808
|
| 117 |
+
"Glyoxylate and dicarboxylate metabolism - Mus musculus (house mouse) Homo sapiens mmu00630",0.0149334993862318,"13382,76238",0.0377199596566027
|
| 118 |
+
"Adherens junction - Mus musculus (house mouse) Homo sapiens mmu04520",0.0154691309793243,"108100,20613,11431",0.0387389348456582
|
| 119 |
+
"Circadian rhythm - Mus musculus (house mouse) Homo sapiens mmu04710",0.0158082462235604,"12234,19079",0.0392526791822305
|
| 120 |
+
"Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse) Homo sapiens mmu04061",0.0168412754094551,"20302,20300,56744",0.0414663335711793
|
| 121 |
+
"DNA replication - Mus musculus (house mouse) Homo sapiens mmu03030",0.0176217905832604,"108167613,16881",0.0426511775862834
|
| 122 |
+
"Renin-angiotensin system - Mus musculus (house mouse) Homo sapiens mmu04614",0.0176217905832604,"11421,70495",0.0426511775862834
|
| 123 |
+
"Hepatocellular carcinoma - Mus musculus (house mouse) Homo sapiens mmu05225",0.0177591933977016,"21803,18803,50493,57265",0.0426511775862834
|
| 124 |
+
"Choline metabolism in cancer - Mus musculus (house mouse) Homo sapiens mmu05231",0.01827935837835,"18803,12651,18805",0.0435435122346062
|
| 125 |
+
"Wnt signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04310",0.0191196941698186,"12234,14735,208846,57265",0.0451779870302972
|
| 126 |
+
"Melanogenesis - Mus musculus (house mouse) Homo sapiens mmu04916",0.0192748121737392,"104111,14681,57265",0.0451801597352446
|
| 127 |
+
"AGE-RAGE signaling pathway in diabetic complications - Mus musculus (house mouse) Homo sapiens mmu04933",0.019783574893119,"21803,18803,13367",0.0460046622514594
|
| 128 |
+
"Glycine, serine and threonine metabolism - Mus musculus (house mouse) Homo sapiens mmu00260",0.0214976369321462,"13382,76238",0.049209434539991
|
| 129 |
+
"Nicotine addiction - Mus musculus (house mouse) Homo sapiens mmu05033",0.0214976369321462,"14395,242443",0.049209434539991
|
| 130 |
+
"Amoebiasis - Mus musculus (house mouse) Homo sapiens mmu05146",0.0229908320912245,"21803,16773,16159",0.0522194868428588
|
| 131 |
+
"Intestinal immune network for IgA production - Mus musculus (house mouse) Homo sapiens mmu04672",0.0246139901992752,"21803,20300",0.0554761471414432
|
| 132 |
+
"Pyruvate metabolism - Mus musculus (house mouse) Homo sapiens mmu00620",0.025691316159277,"13382,76238",0.0569832204005539
|
| 133 |
+
"Vasopressin-regulated water reabsorption - Mus musculus (house mouse) Homo sapiens mmu04962",0.025691316159277,"56455,104111",0.0569832204005539
|
| 134 |
+
"TGF-beta signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04350",0.0258661034582719,"21803,15216,12167",0.0569832204005539
|
| 135 |
+
"Growth hormone synthesis, secretion and action - Mus musculus (house mouse) Homo sapiens mmu04935",0.028925079200595,"18803,104111,20605",0.0630176616875619
|
| 136 |
+
"Proteasome - Mus musculus (house mouse) Homo sapiens mmu03050",0.0290354413918801,"23997,73902",0.0630176616875619
|
| 137 |
+
"Nucleocytoplasmic transport - Mus musculus (house mouse) Homo sapiens mmu03013",0.0295588486274545,"227720,320938,67878",0.0636819312341482
|
| 138 |
+
"Cocaine addiction - Mus musculus (house mouse) Homo sapiens mmu05030",0.0301867188622145,"13385,242443",0.0641201265687858
|
| 139 |
+
"Leukocyte transendothelial migration - Mus musculus (house mouse) Homo sapiens mmu04670",0.0301999230938309,"18803,19303,56508",0.0641201265687858
|
| 140 |
+
"Ether lipid metabolism - Mus musculus (house mouse) Homo sapiens mmu00565",0.0313558795397303,"18805,53357",0.0654656495973279
|
| 141 |
+
"Herpes simplex virus 1 infection - Mus musculus (house mouse) Homo sapiens mmu05168",0.0313645569914615,"19106,21356,16159,15015",0.0654656495973279
|
| 142 |
+
"Neurotrophin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04722",0.0315039474171441,"18803,18036,72843",0.0654656495973279
|
| 143 |
+
"Tryptophan metabolism - Mus musculus (house mouse) Homo sapiens mmu00380",0.034968295275717,"13382,70266",0.072152890956233
|
| 144 |
+
"Inflammatory mediator regulation of TRP channels - Mus musculus (house mouse) Homo sapiens mmu04750",0.0377306349669488,"18803,104111,53357",0.0769519082409901
|
| 145 |
+
"Kaposi sarcoma-associated herpesvirus infection - Mus musculus (house mouse) Homo sapiens mmu05167",0.037819367872705,"18803,19106,15015,14701",0.0769519082409901
|
| 146 |
+
"Mineral absorption - Mus musculus (house mouse) Homo sapiens mmu04978",0.038733231472763,"171429,53945",0.0782678401484108
|
| 147 |
+
"Sphingolipid metabolism - Mus musculus (house mouse) Homo sapiens mmu00600",0.0400210383613077,"14667,19156",0.0803161934237203
|
| 148 |
+
"Estrogen signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04915",0.0406845373906717,"104111,14681,19401",0.0810923092208627
|
| 149 |
+
"N-Glycan biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00510",0.0413248856286418,"53418,13480",0.0812630301288057
|
| 150 |
+
"Regulation of lipolysis in adipocytes - Mus musculus (house mouse) Homo sapiens mmu04923",0.0413248856286418,"104111,67469",0.0812630301288057
|
| 151 |
+
"Apoptosis - Mus musculus (house mouse) Homo sapiens mmu04210",0.0422040245896127,"235587,12366,328417",0.0822029852096957
|
| 152 |
+
"VEGF signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04370",0.0426445520541766,"18803,19303",0.0822029852096957
|
| 153 |
+
"Allograft rejection - Mus musculus (house mouse) Homo sapiens mmu05330",0.0426445520541766,"16159,15015",0.0822029852096957
|
| 154 |
+
"Cytoskeleton in muscle cells - Mus musculus (house mouse) Homo sapiens mmu04820",0.0438319374151194,"16773,13367,208846,11735",0.083939592566209
|
| 155 |
+
"Riboflavin metabolism - Mus musculus (house mouse) Homo sapiens mmu00740",0.0442329490190337,"11431",0.0841574939128369
|
| 156 |
+
"Signaling pathways regulating pluripotency of stem cells - Mus musculus (house mouse) Homo sapiens mmu04550",0.0453273079732431,"22658,57265,12167",0.0851399162809571
|
| 157 |
+
"Long-term depression - Mus musculus (house mouse) Homo sapiens mmu04730",0.0453304673714311,"12921,14681",0.0851399162809571
|
| 158 |
+
"Oxidative phosphorylation - Mus musculus (house mouse) Homo sapiens mmu00190",0.0461255742694992,"27060,12869,17992",0.0855366662086282
|
| 159 |
+
"Spinocerebellar ataxia - Mus musculus (house mouse) Homo sapiens mmu05017",0.0461255742694992,"20513,23997,242443",0.0855366662086282
|
| 160 |
+
"Longevity regulating pathway - multiple species - Mus musculus (house mouse) Homo sapiens mmu04213",0.0466962836503805,"104111,19079",0.0859419838188946
|
| 161 |
+
"Measles - Mus musculus (house mouse) Homo sapiens mmu05162",0.0469307761468366,"19106,16159,18036",0.0859419838188946
|
| 162 |
+
"Inflammatory bowel disease - Mus musculus (house mouse) Homo sapiens mmu05321",0.0480770538318894,"21803,16159",0.0874942656692149
|
| 163 |
+
"Vascular smooth muscle contraction - Mus musculus (house mouse) Homo sapiens mmu04270",0.0485618979283485,"11540,104111,53357",0.0878310869938649
|
| 164 |
+
"Viral life cycle - HIV-1 - Mus musculus (house mouse) Homo sapiens mmu03250",0.0494725664334714,"320938,235180",0.0883869632012629
|
| 165 |
+
"GnRH secretion - Mus musculus (house mouse) Homo sapiens mmu04929",0.0494725664334714,"58226,20750",0.0883869632012629
|
| 166 |
+
"Notch signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04330",0.050882611875482,"59287,11491",0.0903551835122196
|
| 167 |
+
"Type I diabetes mellitus - Mus musculus (house mouse) Homo sapiens mmu04940",0.0523069824664406,"16159,15015",0.0923249750763078
|
| 168 |
+
"Gastric cancer - Mus musculus (house mouse) Homo sapiens mmu05226",0.0536193355118311,"21803,18671,57265",0.0940746425447096
|
| 169 |
+
"RIG-I-like receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04622",0.0641933412252838,"16159,18036",0.111956243922668
|
| 170 |
+
"Pancreatic cancer - Mus musculus (house mouse) Homo sapiens mmu05212",0.068862965835339,"21803,18805",0.119389638992629
|
| 171 |
+
"Inositol phosphate metabolism - Mus musculus (house mouse) Homo sapiens mmu00562",0.0704437059846281,"18803,16332",0.120701788616936
|
| 172 |
+
"Pertussis - Mus musculus (house mouse) Homo sapiens mmu05133",0.0704437059846281,"16159,15900",0.120701788616936
|
| 173 |
+
"Non-homologous end-joining - Mus musculus (house mouse) Homo sapiens mmu03450",0.0708809265091223,"319583",0.12074483411147
|
| 174 |
+
"B cell receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04662",0.0752559400948037,"18036,16332",0.127456592183685
|
| 175 |
+
"Glycosaminoglycan biosynthesis - keratan sulfate - Mus musculus (house mouse) Homo sapiens mmu00533",0.0761208332590591,"53418",0.127596321909287
|
| 176 |
+
"Influenza A - Mus musculus (house mouse) Homo sapiens mmu05164",0.0762094072837038,"19106,16159,18036",0.127596321909287
|
| 177 |
+
"RNA degradation - Mus musculus (house mouse) Homo sapiens mmu03018",0.080169409785013,"66094,66373",0.133463846971641
|
| 178 |
+
"Thiamine metabolism - Mus musculus (house mouse) Homo sapiens mmu00730",0.0813312351883801,"11431",0.134633061639522
|
| 179 |
+
"Phagosome - Mus musculus (house mouse) Homo sapiens mmu04145",0.0834703935301171,"27060,15015,140792",0.137397894968114
|
| 180 |
+
"Insulin secretion - Mus musculus (house mouse) Homo sapiens mmu04911",0.0851793600446299,"104111,56508",0.138653069405981
|
| 181 |
+
"Arrhythmogenic right ventricular cardiomyopathy - Mus musculus (house mouse) Homo sapiens mmu05412",0.0851793600446299,"16773,140723",0.138653069405981
|
| 182 |
+
"Peroxisome - Mus musculus (house mouse) Homo sapiens mmu04146",0.0868699806467782,"20524,111175",0.140623780826
|
| 183 |
+
"PD-L1 expression and PD-1 checkpoint pathway in cancer - Mus musculus (house mouse) Homo sapiens mmu05235",0.088570638384365,"18803,18036",0.142588994761643
|
| 184 |
+
"ECM-receptor interaction - Mus musculus (house mouse) Homo sapiens mmu04512",0.0902811667399195,"16773,20750",0.143385161806229
|
| 185 |
+
"Cardiac muscle contraction - Mus musculus (house mouse) Homo sapiens mmu04260",0.0902811667399195,"12869,140723",0.143385161806229
|
| 186 |
+
"Nitrogen metabolism - Mus musculus (house mouse) Homo sapiens mmu00910",0.0916641871504653,"23831",0.143385161806229
|
| 187 |
+
"Glycosphingolipid biosynthesis - globo and isoglobo series - Mus musculus (house mouse) Homo sapiens mmu00603",0.0916641871504653,"93961",0.143385161806229
|
| 188 |
+
"GnRH signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04912",0.0920014007493891,"104111,18805",0.143385161806229
|
| 189 |
+
"Longevity regulating pathway - Mus musculus (house mouse) Homo sapiens mmu04211",0.0920014007493891,"104111,19079",0.143385161806229
|
| 190 |
+
"Viral myocarditis - Mus musculus (house mouse) Homo sapiens mmu05416",0.0954703335679758,"16773,15015",0.148004273732365
|
| 191 |
+
"Primary bile acid biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00120",0.0967870661434326,"104086",0.148359802402744
|
| 192 |
+
"Other glycan degradation - Mus musculus (house mouse) Homo sapiens mmu00511",0.0967870661434326,"71665",0.148359802402744
|
| 193 |
+
"Progesterone-mediated oocyte maturation - Mus musculus (house mouse) Homo sapiens mmu04914",0.0972187101069175,"104111,17451",0.148359802402744
|
| 194 |
+
"Complement and coagulation cascades - Mus musculus (house mouse) Homo sapiens mmu04610",0.0989761477355028,"12946,18791",0.149484594260321
|
| 195 |
+
"Small cell lung cancer - Mus musculus (house mouse) Homo sapiens mmu05222",0.0989761477355028,"22032,16773",0.149484594260321
|
| 196 |
+
"Lipoic acid metabolism - Mus musculus (house mouse) Homo sapiens mmu00785",0.101881098246601,"13382",0.152475382852257
|
| 197 |
+
"Motor proteins - Mus musculus (house mouse) Homo sapiens mmu04814",0.10226200662684,"56455,286942,668880",0.152475382852257
|
| 198 |
+
"Phosphatidylinositol signaling system - Mus musculus (house mouse) Homo sapiens mmu04070",0.102517578231723,"18803,16332",0.152475382852257
|
| 199 |
+
"IL-17 signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04657",0.104301260776889,"22032,103213",0.154344794988022
|
| 200 |
+
"Mitophagy - animal - Mus musculus (house mouse) Homo sapiens mmu04137",0.111518887129482,"59040,28185",0.163239293492549
|
| 201 |
+
"Bile secretion - Mus musculus (house mouse) Homo sapiens mmu04976",0.111518887129482,"104111,18671",0.163239293492549
|
| 202 |
+
"Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Mus musculus (house mouse) Homo sapiens mmu00532",0.111983269597277,"338362",0.163239293492549
|
| 203 |
+
"Ribosome - Mus musculus (house mouse) Homo sapiens mmu03010",0.115985066845105,"68463,27395,121022,108168832",0.168065640331919
|
| 204 |
+
"Glucagon signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04922",0.117014985077513,"12894,19079",0.168065640331919
|
| 205 |
+
"Aldosterone synthesis and secretion - Mus musculus (house mouse) Homo sapiens mmu04925",0.117014985077513,"104111,58226",0.168065640331919
|
| 206 |
+
"NF-kappa B signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04064",0.122577776983599,"16803,18803",0.175196530030217
|
| 207 |
+
"Glycosaminoglycan biosynthesis - heparan sulfate / heparin - Mus musculus (house mouse) Homo sapiens mmu00534",0.126924199995487,"15531",0.180528109702318
|
| 208 |
+
"Cornified envelope formation - Mus musculus (house mouse) Homo sapiens mmu04382",0.131305500984044,"67469,235542,21770",0.185857544871135
|
| 209 |
+
"Folate biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00790",0.136745119194901,"72562",0.191704880019646
|
| 210 |
+
"Vitamin digestion and absorption - Mus musculus (house mouse) Homo sapiens mmu04977",0.136745119194901,"69698",0.191704880019646
|
| 211 |
+
"Pancreatic secretion - Mus musculus (house mouse) Homo sapiens mmu04972",0.137709469417001,"19340,104111",0.192137497805625
|
| 212 |
+
"Butanoate metabolism - Mus musculus (house mouse) Homo sapiens mmu00650",0.141614138865123,"217666",0.194802547828549
|
| 213 |
+
"Hippo signaling pathway - multiple species - Mus musculus (house mouse) Homo sapiens mmu04392",0.141614138865123,"29806",0.194802547828549
|
| 214 |
+
"Collecting duct acid secretion - Mus musculus (house mouse) Homo sapiens mmu04966",0.141614138865123,"27060",0.194802547828549
|
| 215 |
+
"Thyroid hormone signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04919",0.147363620402916,"18803,107585",0.201764209243245
|
| 216 |
+
"Platelet activation - Mus musculus (house mouse) Homo sapiens mmu04611",0.159122236355045,"104111,108101",0.216850303497805
|
| 217 |
+
"Propanoate metabolism - Mus musculus (house mouse) Homo sapiens mmu00640",0.160817558826275,"13382",0.218146040444901
|
| 218 |
+
"Citrate cycle (TCA cycle) - Mus musculus (house mouse) Homo sapiens mmu00020",0.165551013512596,"13382",0.220483849814502
|
| 219 |
+
"Galactose metabolism - Mus musculus (house mouse) Homo sapiens mmu00052",0.165551013512596,"53418",0.220483849814502
|
| 220 |
+
"RNA polymerase - Mus musculus (house mouse) Homo sapiens mmu03020",0.165551013512596,"231329",0.220483849814502
|
| 221 |
+
"Autophagy - other - Mus musculus (house mouse) Homo sapiens mmu04136",0.165551013512596,"50540",0.220483849814502
|
| 222 |
+
"Osteoclast differentiation - Mus musculus (house mouse) Homo sapiens mmu04380",0.171046199014956,"21803,100201",0.226771657517566
|
| 223 |
+
"Pentose phosphate pathway - Mus musculus (house mouse) Homo sapiens mmu00030",0.174938100665575,"71336",0.22795842227826
|
| 224 |
+
"Biosynthesis of unsaturated fatty acids - Mus musculus (house mouse) Homo sapiens mmu01040",0.174938100665575,"56473",0.22795842227826
|
| 225 |
+
"SNARE interactions in vesicular transport - Mus musculus (house mouse) Homo sapiens mmu04130",0.174938100665575,"53330",0.22795842227826
|
| 226 |
+
"Purine metabolism - Mus musculus (house mouse) Homo sapiens mmu00230",0.175053395947469,"104111,218461",0.22795842227826
|
| 227 |
+
"ATP-dependent chromatin remodeling - Mus musculus (house mouse) Homo sapiens mmu03082",0.179075423330094,"22632,17192",0.232164155025299
|
| 228 |
+
"Insulin signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04910",0.187160632122924,"19079,16332",0.240542059126847
|
| 229 |
+
"Pentose and glucuronate interconversions - Mus musculus (house mouse) Homo sapiens mmu00040",0.188821411601279,"67880",0.240542059126847
|
| 230 |
+
"One carbon pool by folate - Mus musculus (house mouse) Homo sapiens mmu00670",0.188821411601279,"13382",0.240542059126847
|
| 231 |
+
"African trypanosomiasis - Mus musculus (house mouse) Homo sapiens mmu05143",0.188821411601279,"16159",0.240542059126847
|
| 232 |
+
"Aldosterone-regulated sodium reabsorption - Mus musculus (house mouse) Homo sapiens mmu04960",0.19339715365869,"20393",0.245304614813836
|
| 233 |
+
"Alanine, aspartate and glutamate metabolism - Mus musculus (house mouse) Homo sapiens mmu00250",0.197947125157709,"14583",0.248920633782012
|
| 234 |
+
"Amino sugar and nucleotide sugar metabolism - Mus musculus (house mouse) Homo sapiens mmu00520",0.197947125157709,"14583",0.248920633782012
|
| 235 |
+
"Fluid shear stress and atherosclerosis - Mus musculus (house mouse) Homo sapiens mmu05418",0.205523764733473,"18791,12167",0.257343859260288
|
| 236 |
+
"Ferroptosis - Mus musculus (house mouse) Homo sapiens mmu04216",0.206970335312238,"53945",0.258052375516961
|
| 237 |
+
"Homologous recombination - Mus musculus (house mouse) Homo sapiens mmu03440",0.211443861354206,"108167613",0.262512929562637
|
| 238 |
+
"Nicotinate and nicotinamide metabolism - Mus musculus (house mouse) Homo sapiens mmu00760",0.215892191619799,"66454",0.266904692593254
|
| 239 |
+
"Basal transcription factors - Mus musculus (house mouse) Homo sapiens mmu03022",0.220315467793299,"99730",0.271228706148894
|
| 240 |
+
"Various types of N-glycan biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00513",0.229087420628193,"53418",0.28084775834335
|
| 241 |
+
"Porphyrin metabolism - Mus musculus (house mouse) Homo sapiens mmu00860",0.233436376698549,"17025",0.284986909886145
|
| 242 |
+
"Hepatitis B - Mus musculus (house mouse) Homo sapiens mmu05161",0.236501056377566,"21803,54401",0.286342188093499
|
| 243 |
+
"Hepatitis C - Mus musculus (house mouse) Homo sapiens mmu05160",0.236501056377566,"54401,19106",0.286342188093499
|
| 244 |
+
"cGMP-PKG signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04022",0.253129892551332,"104111,11551",0.305214232582471
|
| 245 |
+
"Fatty acid degradation - Mus musculus (house mouse) Homo sapiens mmu00071",0.254816471519121,"12894",0.305988631783207
|
| 246 |
+
"MicroRNAs in cancer - Mus musculus (house mouse) Homo sapiens mmu05206",0.267320420883972,"18803,18671,11987",0.31755718343223
|
| 247 |
+
"Linoleic acid metabolism - Mus musculus (house mouse) Homo sapiens mmu00591",0.267357669902869,"53357",0.31755718343223
|
| 248 |
+
"Cell adhesion molecule (CAM) interaction - Mus musculus (house mouse) Homo sapiens mmu04514",0.267701789446283,"15015,241568",0.31755718343223
|
| 249 |
+
"Pyrimidine metabolism - Mus musculus (house mouse) Homo sapiens mmu00240",0.275601173517463,"320685",0.323004575362467
|
| 250 |
+
"Cysteine and methionine metabolism - Mus musculus (house mouse) Homo sapiens mmu00270",0.275601173517463,"70266",0.323004575362467
|
| 251 |
+
"Valine, leucine and isoleucine degradation - Mus musculus (house mouse) Homo sapiens mmu00280",0.275601173517463,"13382",0.323004575362467
|
| 252 |
+
"ABC transporters - Mus musculus (house mouse) Homo sapiens mmu02010",0.279688131788749,"18671",0.323907599265231
|
| 253 |
+
"Hedgehog signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04340",0.279688131788749,"12234",0.323907599265231
|
| 254 |
+
"Graft-versus-host disease - Mus musculus (house mouse) Homo sapiens mmu05332",0.279688131788749,"15015",0.323907599265231
|
| 255 |
+
"Endocrine and other factor-regulated calcium reabsorption - Mus musculus (house mouse) Homo sapiens mmu04961",0.291811392786502,"11772",0.336617079080492
|
| 256 |
+
"Basal cell carcinoma - Mus musculus (house mouse) Homo sapiens mmu05217",0.299780174320525,"57265",0.344453298336917
|
| 257 |
+
"Lysine degradation - Mus musculus (house mouse) Homo sapiens mmu00310",0.30373092927997,"13382",0.346276896027358
|
| 258 |
+
"Ovarian steroidogenesis - Mus musculus (house mouse) Homo sapiens mmu04913",0.30373092927997,"104111",0.346276896027358
|
| 259 |
+
"Fc epsilon RI signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04664",0.311565797003708,"18803",0.353832474891808
|
| 260 |
+
"Glycolysis / Gluconeogenesis - Mus musculus (house mouse) Homo sapiens mmu00010",0.315450159417662,"13382",0.356860605055501
|
| 261 |
+
"Central carbon metabolism in cancer - Mus musculus (house mouse) Homo sapiens mmu05230",0.323153360225491,"20514",0.362773695578808
|
| 262 |
+
"Amphetamine addiction - Mus musculus (house mouse) Homo sapiens mmu05031",0.323153360225491,"242443",0.362773695578808
|
| 263 |
+
"Acute myeloid leukemia - Mus musculus (house mouse) Homo sapiens mmu05221",0.326972444086767,"19401",0.364269681054839
|
| 264 |
+
"Renal cell carcinoma - Mus musculus (house mouse) Homo sapiens mmu05211",0.326972444086767,"21803",0.364269681054839
|
| 265 |
+
"Non-small cell lung cancer - Mus musculus (house mouse) Homo sapiens mmu05223",0.334546187231929,"18803",0.371295579011194
|
| 266 |
+
"Glutathione metabolism - Mus musculus (house mouse) Homo sapiens mmu00480",0.338301087870911,"14782",0.374046108476139
|
| 267 |
+
"Autoimmune thyroid disease - Mus musculus (house mouse) Homo sapiens mmu05320",0.342034834328669,"15015",0.376594910257876
|
| 268 |
+
"Renin secretion - Mus musculus (house mouse) Homo sapiens mmu04924",0.345747545595115,"11421",0.376594910257876
|
| 269 |
+
"Gastric acid secretion - Mus musculus (house mouse) Homo sapiens mmu04971",0.345747545595115,"104111",0.376594910257876
|
| 270 |
+
"Glioma - Mus musculus (house mouse) Homo sapiens mmu05214",0.345747545595115,"18803",0.376594910257876
|
| 271 |
+
"Chronic myeloid leukemia - Mus musculus (house mouse) Homo sapiens mmu05220",0.349439339991912,"21803",0.379206394880112
|
| 272 |
+
"Chemical carcinogenesis - receptor activation - Mus musculus (house mouse) Homo sapiens mmu05207",0.374511927709835,"104111,71904",0.404915110033142
|
| 273 |
+
"ErbB signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04012",0.378234668884088,"18803",0.407436610231756
|
| 274 |
+
"Gap junction - Mus musculus (house mouse) Homo sapiens mmu04540",0.385232416534745,"104111",0.413454571592235
|
| 275 |
+
"Salivary secretion - Mus musculus (house mouse) Homo sapiens mmu04970",0.388701747184606,"104111",0.415655517974779
|
| 276 |
+
"Colorectal cancer - Mus musculus (house mouse) Homo sapiens mmu05210",0.392151530044378,"21803",0.417819630192737
|
| 277 |
+
"Arachidonic acid metabolism - Mus musculus (house mouse) Homo sapiens mmu00590",0.395581875081929,"53357",0.419947425358714
|
| 278 |
+
"Hematopoietic cell lineage - Mus musculus (house mouse) Homo sapiens mmu04640",0.409111054821737,"12946",0.432742018277144
|
| 279 |
+
"Salmonella infection - Mus musculus (house mouse) Homo sapiens mmu05132",0.414029708046438,"56455,242894",0.436369440494987
|
| 280 |
+
"Steroid hormone biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00140",0.435269060902385,"56448",0.457110519155551
|
| 281 |
+
"Retinol metabolism - Mus musculus (house mouse) Homo sapiens mmu00830",0.438456444962096,"19378",0.458813351335336
|
| 282 |
+
"Prostate cancer - Mus musculus (house mouse) Homo sapiens mmu05215",0.454125954276949,"18791",0.473519233463154
|
| 283 |
+
"Protein digestion and absorption - Mus musculus (house mouse) Homo sapiens mmu04974",0.457207073441462,"20514",0.475041391909037
|
| 284 |
+
"C-type lectin receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04625",0.469358887545955,"16159",0.485944007247225
|
| 285 |
+
"HIF-1 signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04066",0.48416738972325,"18803",0.49951072249617
|
| 286 |
+
"TNF signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04668",0.487079203328975,"11491",0.500751602018911
|
| 287 |
+
"Breast cancer - Mus musculus (house mouse) Homo sapiens mmu05224",0.564744120265574,"57265",0.578566528803542
|
| 288 |
+
"Ribosome biogenesis in eukaryotes - Mus musculus (house mouse) Homo sapiens mmu03008",0.579283600001175,"67619",0.591394058537784
|
| 289 |
+
"JAK-STAT signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04630",0.620056451561917,"16159",0.630821320512645
|
| 290 |
+
"Necroptosis - Mus musculus (house mouse) Homo sapiens mmu04217",0.632750933125029,"19106",0.641508731507383
|
| 291 |
+
"NOD-like receptor signaling pathway - Mus musculus (house mouse) Homo sapiens mmu04621",0.698800397394389,"18036",0.706029367022607
|
| 292 |
+
"Olfactory transduction - Mus musculus (house mouse) Homo sapiens mmu04740",0.912580314278133,"104111,258383,18345,257963",0.91885234392953
|
| 293 |
+
"Aminoacyl-tRNA biosynthesis - Mus musculus (house mouse) Homo sapiens mmu00970",0.9262170726167,"214580",0.929389048892785
|
| 294 |
+
"Spliceosome - Mus musculus (house mouse) Homo sapiens mmu03040",0.936831916565462,"66877,66094,66373",0.936831916565462
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/metadata_3xtg.csv
ADDED
|
@@ -0,0 +1,7 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
sample,condition
|
| 2 |
+
G3R1_Cortex_3xTgAD,3xTgAD
|
| 3 |
+
G3R3_Cortex_3xTgAD,3xTgAD
|
| 4 |
+
G3R4_Cortex_3xTgAD,3xTgAD
|
| 5 |
+
G3R10_Cortex_WT,WT
|
| 6 |
+
G3R7_Cortex_WT,WT
|
| 7 |
+
G3R9_Cortex_WT,WT
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/output_validation.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"postprocess": [
|
| 3 |
+
{
|
| 4 |
+
"file": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/pathway_comparison.csv",
|
| 5 |
+
"actions": [
|
| 6 |
+
"canonicalized_pathway_header"
|
| 7 |
+
]
|
| 8 |
+
}
|
| 9 |
+
],
|
| 10 |
+
"outputs": [
|
| 11 |
+
{
|
| 12 |
+
"path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/pathway_comparison.csv",
|
| 13 |
+
"exists": true,
|
| 14 |
+
"size_bytes": 36083
|
| 15 |
+
}
|
| 16 |
+
]
|
| 17 |
+
}
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/pathway_comparison.csv
ADDED
|
@@ -0,0 +1,349 @@
|
|
|
|
|
|
|
|
|
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|
| 1 |
+
Pathway,5xFAD_pvalue,3xTG_AD_pvalue,PS3O1S_pvalue
|
| 2 |
+
Glycolysis / Gluconeogenesis Homo sapiens mmu00010,1.16007379910011e-07,0.0715586224791162,0.315450159417662
|
| 3 |
+
Citrate cycle (TCA cycle) Homo sapiens mmu00020,0.0004548723811018,,0.165551013512596
|
| 4 |
+
Pentose phosphate pathway Homo sapiens mmu00030,0.0049799815239164,0.387573068984444,0.174938100665575
|
| 5 |
+
Pentose and glucuronate interconversions Homo sapiens mmu00040,8.97431067083743e-06,2.14290481915033e-09,0.188821411601279
|
| 6 |
+
Fructose and mannose metabolism Homo sapiens mmu00051,4.61111037237269e-08,0.0982394640526499,
|
| 7 |
+
Galactose metabolism Homo sapiens mmu00052,1.14004312231722e-08,0.0106614295261939,0.165551013512596
|
| 8 |
+
Ascorbate and aldarate metabolism Homo sapiens mmu00053,0.0273319425829933,4.90218544646341e-13,
|
| 9 |
+
Fatty acid biosynthesis Homo sapiens mmu00061,,0.0298078709333924,
|
| 10 |
+
Fatty acid elongation Homo sapiens mmu00062,2.84765298790708e-05,0.068438877249005,
|
| 11 |
+
Fatty acid degradation Homo sapiens mmu00071,0.0905913527719386,0.0065682227047346,0.254816471519121
|
| 12 |
+
Steroid biosynthesis Homo sapiens mmu00100,4.2941009849543e-05,,
|
| 13 |
+
Primary bile acid biosynthesis Homo sapiens mmu00120,1.098877081424e-06,0.22861333929868,0.0967870661434326
|
| 14 |
+
Ubiquinone and other terpenoid-quinone biosynthesis Homo sapiens mmu00130,0.219810771550366,,0.0020183349607259
|
| 15 |
+
Steroid hormone biosynthesis Homo sapiens mmu00140,0.0011449717877273,2.5737254480782e-09,0.435269060902385
|
| 16 |
+
Oxidative phosphorylation Homo sapiens mmu00190,0.164047288933555,0.328368703531495,0.0461255742694992
|
| 17 |
+
Arginine biosynthesis Homo sapiens mmu00220,0.0680505712689631,0.261275717522459,
|
| 18 |
+
Purine metabolism Homo sapiens mmu00230,1.8965260338312e-08,8.07093548012561e-08,0.175053395947469
|
| 19 |
+
Pyrimidine metabolism Homo sapiens mmu00240,0.11151813771352,0.0484444033673713,0.275601173517463
|
| 20 |
+
"Alanine, aspartate and glutamate metabolism Homo sapiens mmu00250",0.0011554049306683,0.0182498129245091,0.197947125157709
|
| 21 |
+
"Glycine, serine and threonine metabolism Homo sapiens mmu00260",0.0012983790917614,0.01952376221915,0.0214976369321462
|
| 22 |
+
Cysteine and methionine metabolism Homo sapiens mmu00270,2.06473558976074e-05,0.560492883410785,0.275601173517463
|
| 23 |
+
"Valine, leucine and isoleucine degradation Homo sapiens mmu00280",0.0293698879112335,0.0013506724116351,0.275601173517463
|
| 24 |
+
"Valine, leucine and isoleucine biosynthesis Homo sapiens mmu00290",0.0024453851022704,,
|
| 25 |
+
Lysine degradation Homo sapiens mmu00310,0.0100661018991482,0.0022656837891048,0.30373092927997
|
| 26 |
+
Arginine and proline metabolism Homo sapiens mmu00330,1.37261135820985e-05,1.19759819253297e-05,
|
| 27 |
+
Histidine metabolism Homo sapiens mmu00340,0.0001645046960451,0.0059546154912769,
|
| 28 |
+
Tyrosine metabolism Homo sapiens mmu00350,0.0483248120206,0.111939916657735,
|
| 29 |
+
Phenylalanine metabolism Homo sapiens mmu00360,0.0680505712689631,0.261275717522459,
|
| 30 |
+
Tryptophan metabolism Homo sapiens mmu00380,0.0041917942955043,9.27465152904013e-06,0.034968295275717
|
| 31 |
+
"Phenylalanine, tyrosine and tryptophan biosynthesis Homo sapiens mmu00400",0.169860547634496,,
|
| 32 |
+
beta-Alanine metabolism Homo sapiens mmu00410,0.0039881925605464,5.61891927179982e-06,
|
| 33 |
+
Taurine and hypotaurine metabolism Homo sapiens mmu00430,0.0738690852395206,0.0002491249779389,
|
| 34 |
+
Phosphonate and phosphinate metabolism Homo sapiens mmu00440,0.116713829983505,0.0828802106868017,
|
| 35 |
+
Selenocompound metabolism Homo sapiens mmu00450,,0.217408256014336,0.0001144100261664
|
| 36 |
+
D-Amino acid metabolism Homo sapiens mmu00470,0.00016360888353,,
|
| 37 |
+
Glutathione metabolism Homo sapiens mmu00480,0.0038731420827885,0.0040177115142072,0.338301087870911
|
| 38 |
+
Starch and sucrose metabolism Homo sapiens mmu00500,0.0006969889387947,0.396343075027413,
|
| 39 |
+
N-Glycan biosynthesis Homo sapiens mmu00510,0.11151813771352,0.560492883410785,0.0413248856286418
|
| 40 |
+
Other glycan degradation Homo sapiens mmu00511,4.77797958650861e-13,0.0269218401804805,0.0967870661434326
|
| 41 |
+
Mucin type O-glycan biosynthesis Homo sapiens mmu00512,4.19654652451238e-05,0.0106614295261939,0.0140804635503338
|
| 42 |
+
Various types of N-glycan biosynthesis Homo sapiens mmu00513,0.0024449449364117,,0.229087420628193
|
| 43 |
+
Other types of O-glycan biosynthesis Homo sapiens mmu00514,2.83474411632161e-07,0.0266120393743797,5.69086529972916e-06
|
| 44 |
+
Mannose type O-glycan biosynthesis Homo sapiens mmu00515,0.0011363472356608,,0.0074260704077436
|
| 45 |
+
Amino sugar and nucleotide sugar metabolism Homo sapiens mmu00520,2.55770319733112e-10,0.0182498129245091,0.197947125157709
|
| 46 |
+
"Neomycin, kanamycin and gentamicin biosynthesis Homo sapiens mmu00524",0.0040202580452827,0.0695596678420736,
|
| 47 |
+
Glycosaminoglycan degradation Homo sapiens mmu00531,3.64145608418791e-12,0.0359263149284303,
|
| 48 |
+
Glycosaminoglycan biosynthesis Homo sapiens mmu00532,0.0086502530451082,,0.111983269597277
|
| 49 |
+
Glycosaminoglycan biosynthesis Homo sapiens mmu00533,0.0323807963145611,0.182807565890172,0.0761208332590591
|
| 50 |
+
Glycosaminoglycan biosynthesis Homo sapiens mmu00534,0.0859545552860372,,0.126924199995487
|
| 51 |
+
Biosynthesis of various nucleotide sugars Homo sapiens mmu00541,0.0007934626050498,0.261275717522459,0.0062099665153752
|
| 52 |
+
Glycerolipid metabolism Homo sapiens mmu00561,0.0003036961923751,2.92060447631715e-07,
|
| 53 |
+
Inositol phosphate metabolism Homo sapiens mmu00562,5.8321487715319605e-09,0.0248541882738288,0.0704437059846281
|
| 54 |
+
Glycosylphosphatidylinositol (GPI)-anchor biosynthesis Homo sapiens mmu00563,0.462376754196789,0.068438877249005,0.0124406214665916
|
| 55 |
+
Glycerophospholipid metabolism Homo sapiens mmu00564,2.9186179623495e-09,2.91098841073418e-09,2.67290030027644e-05
|
| 56 |
+
Ether lipid metabolism Homo sapiens mmu00565,3.6851752364225503e-09,7.0477468159688e-05,0.0313558795397303
|
| 57 |
+
Arachidonic acid metabolism Homo sapiens mmu00590,3.55488224118131e-08,6.58998183805879e-08,0.395581875081929
|
| 58 |
+
Linoleic acid metabolism Homo sapiens mmu00591,0.102938306539596,0.001148851905675,0.267357669902869
|
| 59 |
+
alpha-Linolenic acid metabolism Homo sapiens mmu00592,0.0922044611045341,0.0004163530630961,0.0087404028497273
|
| 60 |
+
Sphingolipid metabolism Homo sapiens mmu00600,1.73967693706546e-14,0.0001502960903404,0.0400210383613077
|
| 61 |
+
Glycosphingolipid biosynthesis Homo sapiens mmu00601,1.49618159788163e-05,0.0005646418401252,0.0101506077691403
|
| 62 |
+
Glycosphingolipid biosynthesis Homo sapiens mmu00603,0.0003368073591581,0.0241566009272045,0.0916641871504653
|
| 63 |
+
Glycosphingolipid biosynthesis Homo sapiens mmu00604,8.320467353272221e-09,,
|
| 64 |
+
Pyruvate metabolism Homo sapiens mmu00620,0.0020033007568207,0.0004082552923543,0.025691316159277
|
| 65 |
+
Glyoxylate and dicarboxylate metabolism Homo sapiens mmu00630,0.0044655847501484,0.0808006940503487,0.0149334993862318
|
| 66 |
+
Propanoate metabolism Homo sapiens mmu00640,0.0035465275381159,0.0009673937759433,0.160817558826275
|
| 67 |
+
Butanoate metabolism Homo sapiens mmu00650,0.0021104904856749,0.0567806565612424,0.141614138865123
|
| 68 |
+
One carbon pool by folate Homo sapiens mmu00670,9.86562916697645e-05,0.413508351610087,0.188821411601279
|
| 69 |
+
Thiamine metabolism Homo sapiens mmu00730,0.0368636643730356,0.194507746232425,0.0813312351883801
|
| 70 |
+
Riboflavin metabolism Homo sapiens mmu00740,,0.108952266338487,0.0442329490190337
|
| 71 |
+
Nicotinate and nicotinamide metabolism Homo sapiens mmu00760,0.0114672455793914,0.0033129139011533,0.215892191619799
|
| 72 |
+
Pantothenate and CoA biosynthesis Homo sapiens mmu00770,0.0007934626050498,0.0032120707437745,
|
| 73 |
+
Lipoic acid metabolism Homo sapiens mmu00785,0.0064966083608299,0.0298078709333924,0.101881098246601
|
| 74 |
+
Folate biosynthesis Homo sapiens mmu00790,1.18426835460871e-05,,0.136745119194901
|
| 75 |
+
Retinol metabolism Homo sapiens mmu00830,4.89511446742575e-05,1.7305335489918998e-12,0.438456444962096
|
| 76 |
+
Porphyrin metabolism Homo sapiens mmu00860,4.58662341507329e-05,1.1258752098895702e-09,0.233436376698549
|
| 77 |
+
Terpenoid backbone biosynthesis Homo sapiens mmu00900,0.0011363472356608,,
|
| 78 |
+
Nitrogen metabolism Homo sapiens mmu00910,0.0046998814994045,,0.0916641871504653
|
| 79 |
+
Sulfur metabolism Homo sapiens mmu00920,0.203503755797242,,
|
| 80 |
+
Aminoacyl-tRNA biosynthesis Homo sapiens mmu00970,,0.998701482189689,0.9262170726167
|
| 81 |
+
Metabolism of xenobiotics by cytochrome P450 Homo sapiens mmu00980,0.0001672378378594,4.32246355996308e-12,
|
| 82 |
+
Drug metabolism Homo sapiens mmu00982,0.0161772199656856,3.2802962179476696e-11,
|
| 83 |
+
Drug metabolism Homo sapiens mmu00983,0.003659469960226,9.03191504757962e-12,
|
| 84 |
+
Biosynthesis of unsaturated fatty acids Homo sapiens mmu01040,6.0142572383617e-05,0.0125942356805834,0.174938100665575
|
| 85 |
+
ABC transporters Homo sapiens mmu02010,0.000180338659063,0.0096247238175321,0.279688131788749
|
| 86 |
+
Ribosome biogenesis in eukaryotes Homo sapiens mmu03008,0.822934521827145,0.0699181383981639,0.579283600001175
|
| 87 |
+
Ribosome Homo sapiens mmu03010,0.904755003240845,0.101737449620311,0.115985066845105
|
| 88 |
+
Nucleocytoplasmic transport Homo sapiens mmu03013,0.698260660880753,0.0278224143973805,0.0295588486274545
|
| 89 |
+
mRNA surveillance pathway Homo sapiens mmu03015,0.0056714396134414,0.187364781691476,0.0003259466582891
|
| 90 |
+
RNA degradation Homo sapiens mmu03018,0.0280038432151324,0.0315872301062652,0.080169409785013
|
| 91 |
+
RNA polymerase Homo sapiens mmu03020,0.484169141410898,0.076606990380589,0.165551013512596
|
| 92 |
+
Basal transcription factors Homo sapiens mmu03022,0.597583102386211,,0.220315467793299
|
| 93 |
+
DNA replication Homo sapiens mmu03030,0.167755375552114,0.404987570865291,0.0176217905832604
|
| 94 |
+
Spliceosome Homo sapiens mmu03040,0.999982533755008,0.824215051765366,0.936831916565462
|
| 95 |
+
Proteasome Homo sapiens mmu03050,0.0155468307665519,,0.0290354413918801
|
| 96 |
+
Protein export Homo sapiens mmu03060,0.0002040332154543,,0.0017395251955425
|
| 97 |
+
ATP-dependent chromatin remodeling Homo sapiens mmu03082,0.0616447827543476,0.0008126374537237,0.179075423330094
|
| 98 |
+
Polycomb repressive complex Homo sapiens mmu03083,0.0095385706238333,0.0379383213111521,0.0016061025990886
|
| 99 |
+
Viral life cycle Homo sapiens mmu03250,5.99114122001517e-08,3.3456877463893e-05,0.0494725664334714
|
| 100 |
+
Virion Homo sapiens mmu03260,0.186856052659539,0.0085396062920342,
|
| 101 |
+
Virion Homo sapiens mmu03264,,0.0143872294214307,
|
| 102 |
+
Virion Homo sapiens mmu03265,0.296474529085686,8.58121914967601e-05,
|
| 103 |
+
Virion Homo sapiens mmu03266,0.0009230821475904,,
|
| 104 |
+
Virion Homo sapiens mmu03267,0.0024453851022704,,
|
| 105 |
+
Virion Homo sapiens mmu03272,0.000599042725837,0.520755596701581,
|
| 106 |
+
Virion Homo sapiens mmu03273,0.0680505712689631,0.261275717522459,
|
| 107 |
+
PPAR signaling pathway Homo sapiens mmu03320,2.18574764825953e-06,0.0392898821687318,0.0016742642974536
|
| 108 |
+
Base excision repair Homo sapiens mmu03410,0.0155468307665519,0.145574881270385,0.0001473788338225
|
| 109 |
+
Nucleotide excision repair Homo sapiens mmu03420,0.698797537302738,0.56678795312173,0.0043742257136655
|
| 110 |
+
Mismatch repair Homo sapiens mmu03430,0.378597484291773,0.0002981570722589,0.0002905577069258
|
| 111 |
+
Homologous recombination Homo sapiens mmu03440,,0.0030387971821036,0.211443861354206
|
| 112 |
+
Non-homologous end-joining Homo sapiens mmu03450,,0.170937541832337,0.0708809265091223
|
| 113 |
+
Fanconi anemia pathway Homo sapiens mmu03460,0.288196393506123,5.22729753638275e-08,1.17183009858575e-05
|
| 114 |
+
MAPK signaling pathway Homo sapiens mmu04010,1.10147903523608e-41,6.0417579175502e-14,0.0074153765542107
|
| 115 |
+
ErbB signaling pathway Homo sapiens mmu04012,9.86987240726503e-14,2.4703896770552503e-10,0.378234668884088
|
| 116 |
+
Ras signaling pathway Homo sapiens mmu04014,1.14773923179688e-20,1.21461829385185e-13,0.0115315930608717
|
| 117 |
+
Rap1 signaling pathway Homo sapiens mmu04015,2.9128732311608903e-25,7.4109425224617e-12,0.0002371792456943
|
| 118 |
+
Calcium signaling pathway Homo sapiens mmu04020,2.49626187287681e-23,7.919890622648871e-14,0.0034722442499441
|
| 119 |
+
cGMP-PKG signaling pathway Homo sapiens mmu04022,2.7740299153652003e-21,0.0002081134983466,0.253129892551332
|
| 120 |
+
cAMP signaling pathway Homo sapiens mmu04024,1.72753706618348e-23,3.9684733451919004e-15,7.36310490653198e-07
|
| 121 |
+
Cytokine-cytokine receptor interaction Homo sapiens mmu04060,3.8505462720693197e-50,2.6307545603689803e-09,0.0068534953991665
|
| 122 |
+
Viral protein interaction with cytokine and cytokine receptor Homo sapiens mmu04061,5.17623688798422e-26,1.30311153570522e-07,0.0168412754094551
|
| 123 |
+
Chemokine signaling pathway Homo sapiens mmu04062,1.71168692268448e-43,2.72099465176671e-08,1.9208159563733e-06
|
| 124 |
+
NF-kappa B signaling pathway Homo sapiens mmu04064,1.46051701310686e-29,0.0001616984437796,0.122577776983599
|
| 125 |
+
HIF-1 signaling pathway Homo sapiens mmu04066,3.7835334967310204e-23,7.85232961048837e-06,0.48416738972325
|
| 126 |
+
FoxO signaling pathway Homo sapiens mmu04068,5.40343230780844e-15,1.0239437527307e-09,0.0070382412120317
|
| 127 |
+
Phosphatidylinositol signaling system Homo sapiens mmu04070,6.73160879873606e-07,0.012517667395432,0.102517578231723
|
| 128 |
+
Sphingolipid signaling pathway Homo sapiens mmu04071,5.5493212540743005e-24,0.119630070651305,0.0066779755902827
|
| 129 |
+
Phospholipase D signaling pathway Homo sapiens mmu04072,4.41084246404156e-21,1.86661677192342e-06,0.0103883732407557
|
| 130 |
+
Neuroactive ligand-receptor interaction Homo sapiens mmu04080,1.11628634996037e-23,2.65566271921484e-18,5.15672881349604e-07
|
| 131 |
+
Hormone signaling Homo sapiens mmu04081,4.73499438756163e-17,2.32786728148106e-14,6.60387911884491e-08
|
| 132 |
+
Neuroactive ligand signaling Homo sapiens mmu04082,8.51734310090692e-15,1.40968724580365e-18,9.81107023474811e-12
|
| 133 |
+
Cell cycle Homo sapiens mmu04110,1.77345108184136e-07,9.86216186883424e-05,0.0020709657856105
|
| 134 |
+
Oocyte meiosis Homo sapiens mmu04114,9.74639384177702e-12,1.22262951093347e-05,0.0007016633806548
|
| 135 |
+
p53 signaling pathway Homo sapiens mmu04115,3.80738289784488e-07,1.25125130398722e-05,
|
| 136 |
+
Ubiquitin mediated proteolysis Homo sapiens mmu04120,9.8546765568888e-05,9.3528997746854e-05,3.30644983292565e-05
|
| 137 |
+
SNARE interactions in vesicular transport Homo sapiens mmu04130,6.0142572383617e-05,0.387573068984444,0.174938100665575
|
| 138 |
+
Autophagy Homo sapiens mmu04136,0.484169141410898,0.369649215304488,0.165551013512596
|
| 139 |
+
Mitophagy Homo sapiens mmu04137,4.49725193785098e-05,0.0006504278246168,0.111518887129482
|
| 140 |
+
Autophagy Homo sapiens mmu04140,1.16949230947527e-14,0.002973977085453,0.0027044873314176
|
| 141 |
+
Protein processing in endoplasmic reticulum Homo sapiens mmu04141,1.13008863693484e-06,0.476903457680544,8.396517276068641e-09
|
| 142 |
+
Lysosome biogenesis Homo sapiens mmu04142,2.27035771882246e-47,2.11718076319893e-07,3.06384304474036e-10
|
| 143 |
+
Endocytosis Homo sapiens mmu04144,1.1711517963463601e-20,9.55263587318523e-06,2.56928028938638e-05
|
| 144 |
+
Phagosome Homo sapiens mmu04145,1.1750155744088798e-42,2.54420283555379e-06,0.0834703935301171
|
| 145 |
+
Peroxisome Homo sapiens mmu04146,0.103588311414573,0.0366139087911143,0.0868699806467782
|
| 146 |
+
Efferocytosis Homo sapiens mmu04148,1.7561968528083098e-26,2.76411659142866e-10,4.37203242840502e-05
|
| 147 |
+
mTOR signaling pathway Homo sapiens mmu04150,8.086334681782711e-10,1.4184435260219502e-09,0.0126587609908749
|
| 148 |
+
PI3K-Akt signaling pathway Homo sapiens mmu04151,3.28189956137272e-38,2.3816798308044898e-18,0.0012917469306149
|
| 149 |
+
AMPK signaling pathway Homo sapiens mmu04152,1.47211969341995e-10,2.44895136776224e-06,0.0059945199523302
|
| 150 |
+
Apoptosis Homo sapiens mmu04210,2.7074370755691e-33,0.0001629918541342,0.0422040245896127
|
| 151 |
+
Longevity regulating pathway Homo sapiens mmu04211,4.0771047662804e-08,7.1312991110613e-07,0.0920014007493891
|
| 152 |
+
Longevity regulating pathway Homo sapiens mmu04213,3.6291043461657705e-09,2.704475173833e-05,0.0466962836503805
|
| 153 |
+
Apoptosis Homo sapiens mmu04215,0.0004548723811018,0.369649215304488,
|
| 154 |
+
Ferroptosis Homo sapiens mmu04216,1.59553351211067e-06,0.0208455930769211,0.206970335312238
|
| 155 |
+
Necroptosis Homo sapiens mmu04217,3.69248517358231e-25,1.98489034204685e-06,0.632750933125029
|
| 156 |
+
Cellular senescence Homo sapiens mmu04218,8.352459980372481e-25,6.88212606944268e-08,0.0006133164572879
|
| 157 |
+
Cardiac muscle contraction Homo sapiens mmu04260,2.91782809847246e-07,0.0092176530875848,0.0902811667399195
|
| 158 |
+
Adrenergic signaling in cardiomyocytes Homo sapiens mmu04261,2.37958784874646e-16,0.0004507709391104,0.0020142088180682
|
| 159 |
+
Vascular smooth muscle contraction Homo sapiens mmu04270,1.1887832967647801e-09,1.88278106716486e-07,0.0485618979283485
|
| 160 |
+
Wnt signaling pathway Homo sapiens mmu04310,4.69223075286559e-13,5.94144665142164e-08,0.0191196941698186
|
| 161 |
+
Notch signaling pathway Homo sapiens mmu04330,0.0019916474762746,0.0641812508653678,0.050882611875482
|
| 162 |
+
Hedgehog signaling pathway Homo sapiens mmu04340,0.0066851623882752,0.0014608426770425,0.279688131788749
|
| 163 |
+
TGF-beta signaling pathway Homo sapiens mmu04350,1.2898400600084e-15,0.0002215666878891,0.0258661034582719
|
| 164 |
+
Axon guidance Homo sapiens mmu04360,1.38918061633254e-17,2.54420283555379e-06,1.01686425986426e-05
|
| 165 |
+
VEGF signaling pathway Homo sapiens mmu04370,5.78431915118163e-13,1.9346414365785e-05,0.0426445520541766
|
| 166 |
+
Apelin signaling pathway Homo sapiens mmu04371,1.61457981450716e-13,3.75859001886932e-05,0.0012523232467364
|
| 167 |
+
Osteoclast differentiation Homo sapiens mmu04380,6.8846744828262e-60,9.621602688549049e-11,0.171046199014956
|
| 168 |
+
Cornified envelope formation Homo sapiens mmu04382,4.9128279850825394e-11,0.0153916073129754,0.131305500984044
|
| 169 |
+
Hippo signaling pathway Homo sapiens mmu04390,2.0031037524103897e-12,3.44529948658125e-06,3.46751452535817e-07
|
| 170 |
+
Hippo signaling pathway Homo sapiens mmu04392,0.000198491714242,0.0567806565612424,0.141614138865123
|
| 171 |
+
Focal adhesion Homo sapiens mmu04510,2.8731900175061003e-16,1.9715647473048797e-11,0.0060335268511748
|
| 172 |
+
ECM-receptor interaction Homo sapiens mmu04512,3.973944267571991e-09,6.127553123237011e-09,0.0902811667399195
|
| 173 |
+
Cell adhesion molecule (CAM) interaction Homo sapiens mmu04514,8.47195476281161e-32,5.94144665142164e-08,0.267701789446283
|
| 174 |
+
IgSF CAM signaling Homo sapiens mmu04517,4.36208962636793e-33,9.94626792586136e-08,9.84253307353294e-06
|
| 175 |
+
Integrin signaling Homo sapiens mmu04518,1.40915044566554e-17,1.1129424458078399e-12,0.0018507452482774
|
| 176 |
+
Cadherin signaling Homo sapiens mmu04519,1.05321268409539e-18,6.15182387610664e-16,1.45175636008651e-07
|
| 177 |
+
Adherens junction Homo sapiens mmu04520,5.33349489589176e-08,5.57380857062211e-05,0.0154691309793243
|
| 178 |
+
Tight junction Homo sapiens mmu04530,1.03741159856939e-12,0.096708343789317,0.0004274740699094
|
| 179 |
+
Gap junction Homo sapiens mmu04540,2.50191116062776e-09,3.42626335844048e-05,0.385232416534745
|
| 180 |
+
Signaling pathways regulating pluripotency of stem cells Homo sapiens mmu04550,5.32407691226303e-09,2.44421238816576e-11,0.0453273079732431
|
| 181 |
+
Complement and coagulation cascades Homo sapiens mmu04610,1.58543801585797e-23,0.0004219127190172,0.0989761477355028
|
| 182 |
+
Platelet activation Homo sapiens mmu04611,9.46712286106975e-26,9.1024502164734e-05,0.159122236355045
|
| 183 |
+
Antigen processing and presentation Homo sapiens mmu04612,2.8365450058686198e-30,4.59056883902028e-08,0.0014756065970057
|
| 184 |
+
Neutrophil extracellular trap formation Homo sapiens mmu04613,1.0147293327207e-26,0.0002432310855087,0.0012887413045722
|
| 185 |
+
Renin-angiotensin system Homo sapiens mmu04614,0.0061247239628189,0.0017113325812488,0.0176217905832604
|
| 186 |
+
Toll-like receptor signaling pathway Homo sapiens mmu04620,3.5242818273324596e-34,0.0001326748069459,0.002950983621268
|
| 187 |
+
NOD-like receptor signaling pathway Homo sapiens mmu04621,1.6829104804391601e-47,0.0010652186562061,0.698800397394389
|
| 188 |
+
RIG-I-like receptor signaling pathway Homo sapiens mmu04622,1.58709923030435e-12,0.0873808655139507,0.0641933412252838
|
| 189 |
+
Cytosolic DNA-sensing pathway Homo sapiens mmu04623,1.74080658951735e-17,0.0303980934801686,0.0113674752838335
|
| 190 |
+
C-type lectin receptor signaling pathway Homo sapiens mmu04625,3.76428215463519e-30,0.0002215666878891,0.469358887545955
|
| 191 |
+
JAK-STAT signaling pathway Homo sapiens mmu04630,5.640071916977249e-28,0.0008705421156036,0.620056451561917
|
| 192 |
+
Hematopoietic cell lineage Homo sapiens mmu04640,2.62233343434477e-33,1.04423216192305e-07,0.409111054821737
|
| 193 |
+
Natural killer cell mediated cytotoxicity Homo sapiens mmu04650,3.89884559514692e-08,0.22861333929868,
|
| 194 |
+
IL-17 signaling pathway Homo sapiens mmu04657,1.50475354787807e-10,0.000510305386979,0.104301260776889
|
| 195 |
+
Th1 and Th2 cell differentiation Homo sapiens mmu04658,6.539934040204819e-30,5.12190457384604e-06,0.0137416979305425
|
| 196 |
+
Th17 cell differentiation Homo sapiens mmu04659,8.852462862439749e-40,2.16917521442013e-05,0.0030543624048625
|
| 197 |
+
T cell receptor signaling pathway Homo sapiens mmu04660,4.8759718777674495e-30,7.09318356488919e-05,0.0006762438665098
|
| 198 |
+
B cell receptor signaling pathway Homo sapiens mmu04662,6.20892398634668e-33,2.12599977176964e-08,0.0752559400948037
|
| 199 |
+
Fc epsilon RI signaling pathway Homo sapiens mmu04664,1.92979512141877e-22,0.0003725743047623,0.311565797003708
|
| 200 |
+
Fc gamma R-mediated phagosome formation Homo sapiens mmu04666,1.63718348946169e-27,6.50030771925069e-05,1.67891012402318e-05
|
| 201 |
+
TNF signaling pathway Homo sapiens mmu04668,6.33870155045936e-32,8.46976482652652e-06,0.487079203328975
|
| 202 |
+
Leukocyte transendothelial migration Homo sapiens mmu04670,2.0529888515950702e-19,0.0016985712276481,0.0301999230938309
|
| 203 |
+
Intestinal immune network for IgA production Homo sapiens mmu04672,9.82116142505938e-14,0.0033129139011533,0.0246139901992752
|
| 204 |
+
Circadian rhythm Homo sapiens mmu04710,0.0320029587058611,0.0013781776261786,0.0158082462235604
|
| 205 |
+
Circadian entrainment Homo sapiens mmu04713,2.2023605098340802e-09,2.21468808502379e-07,0.0025613458499757
|
| 206 |
+
Thermogenesis Homo sapiens mmu04714,0.0106134304361725,4.72102802988879e-05,0.0004492451474131
|
| 207 |
+
Long-term potentiation Homo sapiens mmu04720,1.08793555625182e-06,0.0027708361415107,
|
| 208 |
+
Synaptic vesicle cycle Homo sapiens mmu04721,0.0010307718663953,1.52175684318274e-05,0.0009785890780339
|
| 209 |
+
Neurotrophin signaling pathway Homo sapiens mmu04722,7.060834554855521e-15,1.98601938009334e-07,0.0315039474171441
|
| 210 |
+
Retrograde endocannabinoid signaling Homo sapiens mmu04723,7.229065975061639e-11,8.40090547854639e-05,0.0019041123336009
|
| 211 |
+
Glutamatergic synapse Homo sapiens mmu04724,2.3262184610303602e-17,1.08769061586757e-06,3.89052619042805e-07
|
| 212 |
+
Cholinergic synapse Homo sapiens mmu04725,1.57422636689661e-16,8.38724348632934e-07,0.0040980287701399
|
| 213 |
+
Serotonergic synapse Homo sapiens mmu04726,9.39890374386714e-13,1.04876430531837e-07,0.0011375320303661
|
| 214 |
+
GABAergic synapse Homo sapiens mmu04727,5.5461635104456e-11,6.7623208252869e-06,0.001816563850886
|
| 215 |
+
Dopaminergic synapse Homo sapiens mmu04728,1.0209097960922299e-13,5.11970540410671e-06,0.0011375320303661
|
| 216 |
+
Long-term depression Homo sapiens mmu04730,1.57043649113451e-11,1.89570716582126e-07,0.0453304673714311
|
| 217 |
+
Olfactory transduction Homo sapiens mmu04740,0.999999783530653,0.828879702177402,0.912580314278133
|
| 218 |
+
Taste transduction Homo sapiens mmu04742,0.0001175565524281,0.0435075057870138,0.0001842274519371
|
| 219 |
+
Phototransduction Homo sapiens mmu04744,0.105078120804701,0.0066283621976709,
|
| 220 |
+
Inflammatory mediator regulation of TRP channels Homo sapiens mmu04750,2.18061938277614e-10,3.07754647300385e-06,0.0377306349669488
|
| 221 |
+
Regulation of actin cytoskeleton Homo sapiens mmu04810,4.5823123396568195e-18,8.86410338019016e-06,6.34326748019767e-05
|
| 222 |
+
Motor proteins Homo sapiens mmu04814,4.28243913107307e-12,1.89698131781588e-13,0.10226200662684
|
| 223 |
+
Cytoskeleton in muscle cells Homo sapiens mmu04820,6.3973450402439405e-21,6.69002484639522e-13,0.0438319374151194
|
| 224 |
+
Insulin signaling pathway Homo sapiens mmu04910,6.53437889179828e-22,6.30635034948743e-06,0.187160632122924
|
| 225 |
+
Insulin secretion Homo sapiens mmu04911,2.50191116062776e-09,0.0080077339268897,0.0851793600446299
|
| 226 |
+
GnRH signaling pathway Homo sapiens mmu04912,2.73863251976145e-14,7.1312991110613e-07,0.0920014007493891
|
| 227 |
+
Ovarian steroidogenesis Homo sapiens mmu04913,4.87350934259658e-05,3.77138066878303e-06,0.30373092927997
|
| 228 |
+
Progesterone-mediated oocyte maturation Homo sapiens mmu04914,1.9134743595836702e-17,0.0022573314732602,0.0972187101069175
|
| 229 |
+
Estrogen signaling pathway Homo sapiens mmu04915,4.5495178487480896e-11,0.0001457034114713,0.0406845373906717
|
| 230 |
+
Melanogenesis Homo sapiens mmu04916,6.90577305836819e-06,0.0032459645762106,0.0192748121737392
|
| 231 |
+
Prolactin signaling pathway Homo sapiens mmu04917,7.07091763619115e-24,0.0006896124682863,
|
| 232 |
+
Thyroid hormone synthesis Homo sapiens mmu04918,2.07706010843626e-05,0.0042588781117377,0.0086001529698633
|
| 233 |
+
Thyroid hormone signaling pathway Homo sapiens mmu04919,6.46957591188656e-13,0.0003542607754989,0.147363620402916
|
| 234 |
+
Adipocytokine signaling pathway Homo sapiens mmu04920,5.42569576238322e-15,0.0005958337640781,0.0079780981576433
|
| 235 |
+
Oxytocin signaling pathway Homo sapiens mmu04921,1.5645667291728098e-18,1.20785746333224e-13,0.0019041123336009
|
| 236 |
+
Glucagon signaling pathway Homo sapiens mmu04922,4.4016511656514803e-10,0.0171730061999729,0.117014985077513
|
| 237 |
+
Regulation of lipolysis in adipocytes Homo sapiens mmu04923,1.58901334221195e-09,0.0013506724116351,0.0413248856286418
|
| 238 |
+
Renin secretion Homo sapiens mmu04924,3.81208414321823e-10,1.25125130398722e-05,0.345747545595115
|
| 239 |
+
Aldosterone synthesis and secretion Homo sapiens mmu04925,1.6029278104226e-06,0.0007742598376684,0.117014985077513
|
| 240 |
+
Relaxin signaling pathway Homo sapiens mmu04926,1.61598870577948e-20,0.0029223048201087,0.000931531883993
|
| 241 |
+
Cortisol synthesis and secretion Homo sapiens mmu04927,0.0001140828473494,0.0846485700973768,0.0079780981576433
|
| 242 |
+
"Parathyroid hormone synthesis, secretion and action Homo sapiens mmu04928",2.77234400166648e-10,1.24613161304067e-07,0.0005378942703354
|
| 243 |
+
GnRH secretion Homo sapiens mmu04929,7.64147500566098e-15,0.01277942255874,0.0494725664334714
|
| 244 |
+
Type II diabetes mellitus Homo sapiens mmu04930,5.49244912913205e-13,0.0314383182249157,
|
| 245 |
+
Insulin resistance Homo sapiens mmu04931,1.03579406450291e-14,0.0213315983675432,0.0036084634732197
|
| 246 |
+
Non-alcoholic fatty liver disease Homo sapiens mmu04932,2.5336353289645597e-11,0.0298544987604582,0.0137615868731135
|
| 247 |
+
AGE-RAGE signaling pathway in diabetic complications Homo sapiens mmu04933,8.69829833943995e-28,0.0153115948998531,0.019783574893119
|
| 248 |
+
Cushing syndrome Homo sapiens mmu04934,1.82141016089514e-10,7.32263721136587e-07,0.0023723908211622
|
| 249 |
+
"Growth hormone synthesis, secretion and action Homo sapiens mmu04935",3.7835334967310204e-23,7.85232961048837e-06,0.028925079200595
|
| 250 |
+
Alcoholic liver disease Homo sapiens mmu04936,8.138333383994539e-22,1.91931367862716e-08,0.0086070583454657
|
| 251 |
+
Type I diabetes mellitus Homo sapiens mmu04940,1.2821700557637e-22,3.84498068039579e-07,0.0523069824664406
|
| 252 |
+
Maturity onset diabetes of the young Homo sapiens mmu04950,0.105078120804701,0.0567806565612424,
|
| 253 |
+
Aldosterone-regulated sodium reabsorption Homo sapiens mmu04960,0.0001151282139742,0.0020965610652301,0.19339715365869
|
| 254 |
+
Endocrine and other factor-regulated calcium reabsorption Homo sapiens mmu04961,0.0364244805558484,0.0571781158255804,0.291811392786502
|
| 255 |
+
Vasopressin-regulated water reabsorption Homo sapiens mmu04962,0.0002651661013789,0.0250986131552437,0.025691316159277
|
| 256 |
+
Proximal tubule bicarbonate reclamation Homo sapiens mmu04964,0.0009541224293433,,
|
| 257 |
+
Collecting duct acid secretion Homo sapiens mmu04966,0.0173749611421696,0.0567806565612424,0.141614138865123
|
| 258 |
+
Salivary secretion Homo sapiens mmu04970,2.26375637207734e-07,0.0002625673952954,0.388701747184606
|
| 259 |
+
Gastric acid secretion Homo sapiens mmu04971,3.80738289784488e-07,0.0007405837961595,0.345747545595115
|
| 260 |
+
Pancreatic secretion Homo sapiens mmu04972,7.5547878366619e-07,0.227952223412653,0.137709469417001
|
| 261 |
+
Carbohydrate digestion and absorption Homo sapiens mmu04973,3.6851752364225503e-09,0.155532890498634,
|
| 262 |
+
Protein digestion and absorption Homo sapiens mmu04974,2.39890593046267e-06,2.71767061917917e-05,0.457207073441462
|
| 263 |
+
Fat digestion and absorption Homo sapiens mmu04975,2.52367763649752e-05,0.0236330290602521,
|
| 264 |
+
Bile secretion Homo sapiens mmu04976,1.64413850764691e-07,2.62884922510591e-08,0.111518887129482
|
| 265 |
+
Vitamin digestion and absorption Homo sapiens mmu04977,0.415992390459541,0.312670472856016,0.136745119194901
|
| 266 |
+
Mineral absorption Homo sapiens mmu04978,6.99428127964152e-11,0.186094584417396,0.038733231472763
|
| 267 |
+
Cholesterol metabolism Homo sapiens mmu04979,1.40531524367989e-16,0.165615461244665,0.0030393844354092
|
| 268 |
+
Cobalamin transport and metabolism Homo sapiens mmu04980,0.296474529085686,,
|
| 269 |
+
Folate transport and metabolism Homo sapiens mmu04981,0.000198491714242,0.0567806565612424,
|
| 270 |
+
Alzheimer disease Homo sapiens mmu05010,2.28621598179722e-21,1.74602901806789e-05,0.0070538975574024
|
| 271 |
+
Parkinson disease Homo sapiens mmu05012,3.16161796589871e-07,1.24120376659142e-05,0.0010252887367116
|
| 272 |
+
Amyotrophic lateral sclerosis Homo sapiens mmu05014,1.18813815514367e-06,3.68966062722995e-05,0.00031765193361
|
| 273 |
+
Huntington disease Homo sapiens mmu05016,2.53822198474667e-05,0.000585670284035,0.000410053884325
|
| 274 |
+
Spinocerebellar ataxia Homo sapiens mmu05017,0.0001675675156519,0.0163834053770796,0.0461255742694992
|
| 275 |
+
Prion disease Homo sapiens mmu05020,4.89088035621487e-16,0.0064918878498701,0.0048256434086061
|
| 276 |
+
Pathways of neurodegeneration Homo sapiens mmu05022,5.73523293002421e-17,3.04218091842835e-09,2.38706044331941e-05
|
| 277 |
+
Cocaine addiction Homo sapiens mmu05030,5.27495539392631e-05,1.40383459786205e-09,0.0301867188622145
|
| 278 |
+
Amphetamine addiction Homo sapiens mmu05031,1.16704377828391e-05,5.56013039451753e-08,0.323153360225491
|
| 279 |
+
Morphine addiction Homo sapiens mmu05032,7.76424729544767e-10,1.04423216192305e-07,1.57924334204489e-05
|
| 280 |
+
Nicotine addiction Homo sapiens mmu05033,0.000154585803017,2.15859637277815e-05,0.0214976369321462
|
| 281 |
+
Alcoholism Homo sapiens mmu05034,1.8696027010056198e-12,2.49423903792594e-10,2.7653851469775e-05
|
| 282 |
+
Bacterial invasion of epithelial cells Homo sapiens mmu05100,3.99899391471502e-06,0.0050441253970617,0.0095852102369972
|
| 283 |
+
Salmonella infection Homo sapiens mmu05132,1.76782336830108e-39,1.78858913012443e-07,0.414029708046438
|
| 284 |
+
Pertussis Homo sapiens mmu05133,4.68510873290689e-32,0.302093763789309,0.0704437059846281
|
| 285 |
+
Legionellosis Homo sapiens mmu05134,4.3252699411755e-14,0.572992913720444,0.0045894613363335
|
| 286 |
+
Yersinia infection Homo sapiens mmu05135,9.80652571311148e-31,0.0008126374537237,0.0076023208214864
|
| 287 |
+
Leishmaniasis Homo sapiens mmu05140,3.00554992438239e-35,0.0181975374287284,0.0006839373975029
|
| 288 |
+
Chagas disease Homo sapiens mmu05142,7.31616594102413e-48,0.0610519329903192,0.0003117105205961
|
| 289 |
+
African trypanosomiasis Homo sapiens mmu05143,0.0009047747850169,1.35612174708385e-05,0.188821411601279
|
| 290 |
+
Malaria Homo sapiens mmu05144,6.24995679129593e-11,4.53741109174724e-05,0.0062753049619624
|
| 291 |
+
Toxoplasmosis Homo sapiens mmu05145,3.91840988740042e-36,0.0010213279496008,0.0004046434542687
|
| 292 |
+
Amoebiasis Homo sapiens mmu05146,7.48734086154e-11,0.0191783805314038,0.0229908320912245
|
| 293 |
+
Staphylococcus aureus infection Homo sapiens mmu05150,2.1122065965053901e-19,2.12101835625704e-05,
|
| 294 |
+
Tuberculosis Homo sapiens mmu05152,4.2149792385833e-52,0.0156053764391674,0.003723950648135
|
| 295 |
+
Hepatitis C Homo sapiens mmu05160,9.919043873808771e-35,0.0006466583598337,0.236501056377566
|
| 296 |
+
Hepatitis B Homo sapiens mmu05161,1.56769237912602e-27,8.4182206527415e-07,0.236501056377566
|
| 297 |
+
Measles Homo sapiens mmu05162,1.09118794020101e-37,2.1012403646219e-08,0.0469307761468366
|
| 298 |
+
Human cytomegalovirus infection Homo sapiens mmu05163,5.53506625758267e-45,2.11718076319893e-07,0.0006597595667515
|
| 299 |
+
Influenza A Homo sapiens mmu05164,5.8757842090674495e-49,1.64005074388222e-06,0.0762094072837038
|
| 300 |
+
Human papillomavirus infection Homo sapiens mmu05165,4.29326397489135e-41,5.12298833915413e-17,1.1905573282264e-06
|
| 301 |
+
Human T-cell leukemia virus 1 infection Homo sapiens mmu05166,7.12803658722876e-51,1.90999104316981e-12,0.0131490284129182
|
| 302 |
+
Kaposi sarcoma-associated herpesvirus infection Homo sapiens mmu05167,5.2959711178454e-45,1.49287526318892e-11,0.037819367872705
|
| 303 |
+
Herpes simplex virus 1 infection Homo sapiens mmu05168,3.54655633796264e-61,1.24286012962292e-08,0.0313645569914615
|
| 304 |
+
Epstein-Barr virus infection Homo sapiens mmu05169,1.96764693618455e-62,3.86229482659999e-13,0.0097073553835204
|
| 305 |
+
Human immunodeficiency virus 1 infection Homo sapiens mmu05170,4.02897229235446e-50,4.67749145654413e-10,1.11221744409193e-05
|
| 306 |
+
Coronavirus disease Homo sapiens mmu05171,1.22903099639248e-32,0.0012241802815646,0.0031223841782865
|
| 307 |
+
Pathways in cancer Homo sapiens mmu05200,4.16167044625026e-39,6.87422082517189e-24,0.000343836184543
|
| 308 |
+
Transcriptional misregulation in cancer Homo sapiens mmu05202,6.55616551643516e-20,4.15423660675825e-06,0.0083988612986695
|
| 309 |
+
Viral carcinogenesis Homo sapiens mmu05203,1.43068825249394e-29,1.19637793518929e-06,4.97257421258577e-05
|
| 310 |
+
Chemical carcinogenesis Homo sapiens mmu05204,0.0377965526796061,5.99291367967882e-10,
|
| 311 |
+
Proteoglycans in cancer Homo sapiens mmu05205,5.17895735092886e-25,8.65683380007442e-09,0.0001771623291373
|
| 312 |
+
MicroRNAs in cancer Homo sapiens mmu05206,1.64665656175391e-10,2.44506698880868e-07,0.267320420883972
|
| 313 |
+
Chemical carcinogenesis Homo sapiens mmu05207,1.91624256193048e-11,5.58126569924988e-13,0.374511927709835
|
| 314 |
+
Chemical carcinogenesis Homo sapiens mmu05208,1.91463028348079e-17,6.9347563678937e-06,0.0100551237613953
|
| 315 |
+
Colorectal cancer Homo sapiens mmu05210,3.26579101516989e-11,5.12190457384604e-06,0.392151530044378
|
| 316 |
+
Renal cell carcinoma Homo sapiens mmu05211,9.32825058288915e-05,7.33742455225235e-07,0.326972444086767
|
| 317 |
+
Pancreatic cancer Homo sapiens mmu05212,3.07750947790352e-12,0.0047718586746718,0.068862965835339
|
| 318 |
+
Endometrial cancer Homo sapiens mmu05213,2.68269961107506e-06,0.0001828675983166,
|
| 319 |
+
Glioma Homo sapiens mmu05214,4.17940562551811e-08,1.25425134780085e-07,0.345747545595115
|
| 320 |
+
Prostate cancer Homo sapiens mmu05215,6.78884426191769e-10,2.52309427369761e-05,0.454125954276949
|
| 321 |
+
Thyroid cancer Homo sapiens mmu05216,0.0009047747850169,0.0001779942994763,
|
| 322 |
+
Basal cell carcinoma Homo sapiens mmu05217,0.370609503688799,0.0021132845844196,0.299780174320525
|
| 323 |
+
Melanoma Homo sapiens mmu05218,2.48472855210644e-07,9.36034829627951e-07,
|
| 324 |
+
Bladder cancer Homo sapiens mmu05219,0.0001779582700094,2.4980011097082e-05,
|
| 325 |
+
Chronic myeloid leukemia Homo sapiens mmu05220,4.58458184249154e-10,0.0007944165178449,0.349439339991912
|
| 326 |
+
Acute myeloid leukemia Homo sapiens mmu05221,4.62650802320484e-19,0.0181975374287284,0.326972444086767
|
| 327 |
+
Small cell lung cancer Homo sapiens mmu05222,3.76450243869314e-06,1.1544118019059e-08,0.0989761477355028
|
| 328 |
+
Non-small cell lung cancer Homo sapiens mmu05223,2.1442335081757e-06,8.43429766505529e-08,0.334546187231929
|
| 329 |
+
Breast cancer Homo sapiens mmu05224,1.6649099414170102e-09,5.3626435544696795e-11,0.564744120265574
|
| 330 |
+
Hepatocellular carcinoma Homo sapiens mmu05225,4.5452886576527505e-09,6.2746250842311205e-09,0.0177591933977016
|
| 331 |
+
Gastric cancer Homo sapiens mmu05226,3.3034380385013004e-10,5.4626640020582705e-09,0.0536193355118311
|
| 332 |
+
Central carbon metabolism in cancer Homo sapiens mmu05230,6.22099215160713e-13,0.0031498751298592,0.323153360225491
|
| 333 |
+
Choline metabolism in cancer Homo sapiens mmu05231,1.41429681205156e-13,1.86332482192639e-08,0.01827935837835
|
| 334 |
+
PD-L1 expression and PD-1 checkpoint pathway in cancer Homo sapiens mmu05235,6.539934040204819e-30,0.0017042423569549,0.088570638384365
|
| 335 |
+
Asthma Homo sapiens mmu05310,9.44895912604842e-10,0.0494417443857017,
|
| 336 |
+
Autoimmune thyroid disease Homo sapiens mmu05320,1.68138131989674e-18,0.0006896124682863,0.342034834328669
|
| 337 |
+
Inflammatory bowel disease Homo sapiens mmu05321,9.94857613461502e-22,0.0019684940234023,0.0480770538318894
|
| 338 |
+
Systemic lupus erythematosus Homo sapiens mmu05322,8.87825354860552e-16,1.2164244685538e-05,0.010626487476031
|
| 339 |
+
Rheumatoid arthritis Homo sapiens mmu05323,6.829868242422729e-26,0.0002625673952954,0.0133279844533338
|
| 340 |
+
Allograft rejection Homo sapiens mmu05330,1.35613709163516e-19,0.0001828675983166,0.0426445520541766
|
| 341 |
+
Graft-versus-host disease Homo sapiens mmu05332,5.07173438581654e-21,0.0001828675983166,0.279688131788749
|
| 342 |
+
Primary immunodeficiency Homo sapiens mmu05340,9.700112844338329e-11,0.0147142914948699,
|
| 343 |
+
Hypertrophic cardiomyopathy Homo sapiens mmu05410,1.4598714851459e-07,0.0001007831729276,0.0002718145183344
|
| 344 |
+
Arrhythmogenic right ventricular cardiomyopathy Homo sapiens mmu05412,1.09298184576392e-05,0.0015145178910448,0.0851793600446299
|
| 345 |
+
Dilated cardiomyopathy Homo sapiens mmu05414,2.74440389524853e-08,0.0001240141681763,0.0028500206611534
|
| 346 |
+
Diabetic cardiomyopathy Homo sapiens mmu05415,1.3190317496998501e-14,0.0132550069101062,0.0015232007799588
|
| 347 |
+
Viral myocarditis Homo sapiens mmu05416,1.48965766302555e-17,7.4005993646742e-06,0.0954703335679758
|
| 348 |
+
Lipid and atherosclerosis Homo sapiens mmu05417,1.61144126163139e-39,8.11012722649304e-05,0.0015591762029214
|
| 349 |
+
Fluid shear stress and atherosclerosis Homo sapiens mmu05418,3.4843680985173896e-22,6.37290924339265e-05,0.205523764733473
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/retrieval_plan.json
ADDED
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@@ -0,0 +1,1364 @@
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| 1 |
+
{
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| 2 |
+
"query": "You are running a bioagent-bench task with local files already prepared.\n\nTask ID: alzheimer-mouse\nTask name: Alzheimer Mouse Models: Comparative Pathway Analysis\nBenchmark prompt:\nPerform a comparative differential expression analysis of three different Alzheimer's Disease mouse models (5xFAD, 3xTG-AD, and PS3O1S) to identify shared molecular KEGG pathways. The output should be a CSV file with the following columns: 'pathway','5xFAD_pvalue','3xTG_AD_pvalue','PS3O1S_pvalue'. Example csv <example>Pathway,5xFAD_pvalue,3xTG_AD_pvalue,PS3O1S_pvalue\nPhagosome Homo sapiens hsa04145,1.5045916403148935e-09,0.3102788532065793,0.4443015705596512\n</example> \nData background:\nAnalyze 5xFAD, 3xTG-AD, and PS301S mouse models: normalize counts, perform differential expression, run KEGG pathway enrichment, and compare shared pathways across models.\n\nConstraints:\n1. Use only the benchmark inputs and references explicitly listed below.\n2. Save the required final deliverables exactly to the paths listed below.\n3. Save all intermediate scripts, logs, and scratch outputs inside this run directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826\n4. Keep final deliverables in the same schema/format requested by the benchmark prompt.\n5. Return a concise final summary after writing the required files.\n\nTask-specific instruction:\nUse the provided mouse count and DEA files as inputs. Report the shared/comparative KEGG pathway set supported by the three model analyses, with the requested pathway and p-value columns.\n\nBenchmark data policy:\n- Allowed input data directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data\n- Allowed reference directory: <none>\n- Allowed scratch/output directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826\n- Forbidden truth/results directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/results\n- Forbidden sibling benchmark task directories: /225040511/project/bioagent-bench/dataset/<any task other than alzheimer-mouse>\n- Do not inspect previous bioagent-bench-runs or sibling task outputs as data sources.\n- Do not download external databases or install new packages during the benchmark run.\n\nInput data directory:\n/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data\nVisible input files:\n- DEA_PS3O1S.csv\n- GSE161904_Raw_gene_counts_cortex.txt\n- GSE168137_countList.txt\n\nReference data directory:\n<none>\nVisible reference files:\n- <none>\n\nRequired final output paths:\n- pathway_comparison.csv: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/pathway_comparison.csv",
|
| 3 |
+
"query_context": {},
|
| 4 |
+
"mcp_config": "/225040511/project/Biomni/experiments/bioagent_bench/configs/mcp_scale_1000.yaml",
|
| 5 |
+
"planning_context_text": "{\"prompt\": \"You are running a bioagent-bench task with local files already prepared.\\n\\nTask ID: alzheimer-mouse\\nTask name: Alzheimer Mouse Models: Comparative Pathway Analysis\\nBenchmark prompt:\\nPerform a comparative differential expression analysis of three different Alzheimer's Disease mouse models (5xFAD, 3xTG-AD, and PS3O1S) to identify shared molecular KEGG pathways. The output should be a CSV file with the following columns: 'pathway','5xFAD_pvalue','3xTG_AD_pvalue','PS3O1S_pvalue'. Example csv <example>Pathway,5xFAD_pvalue,3xTG_AD_pvalue,PS3O1S_pvalue\\nPhagosome Homo sapiens hsa04145,1.5045916403148935e-09,0.3102788532065793,0.4443015705596512\\n</example> \\nData background:\\nAnalyze 5xFAD, 3xTG-AD, and PS301S mouse models: normalize counts, perform differential expression, run KEGG pathway enrichment, and compare shared pathways across models.\\n\\nConstraints:\\n1. Use only the benchmark inputs and references explicitly listed below.\\n2. Save the required final deliverables exactly to the paths listed below.\\n3. Save all intermediate scripts, logs, and scratch outputs inside this run directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826\\n4. Keep final deliverables in the same schema/format requested by the benchmark prompt.\\n5. Return a concise final summary after writing the required files.\\n\\nTask-specific instruction:\\nUse the provided mouse count and DEA files as inputs. Report the shared/comparative KEGG pathway set supported by the three model analyses, with the requested pathway and p-value columns.\\n\\nBenchmark data policy:\\n- Allowed input data directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data\\n- Allowed reference directory: <none>\\n- Allowed scratch/output directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826\\n- Forbidden truth/results directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/results\\n- Forbidden sibling benchmark task directories: /225040511/project/bioagent-bench/dataset/<any task other than alzheimer-mouse>\\n- Do not inspect previous bioagent-bench-runs or sibling task outputs as data sources.\\n- Do not download external databases or install new packages during the benchmark run.\\n\\nInput data directory:\\n/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data\\nVisible input files:\\n- DEA_PS3O1S.csv\\n- GSE161904_Raw_gene_counts_cortex.txt\\n- GSE168137_countList.txt\\n\\nReference data directory:\\n<none>\\nVisible reference files:\\n- <none>\\n\\nRequired final output paths:\\n- pathway_comparison.csv: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/pathway_comparison.csv\", \"selected_resources_names\": {\"tools\": [{\"description\": \"Executes the provided Python command in the notebook environment and returns the output.\", \"name\": \"run_python_repl\", \"optional_parameters\": [], \"required_parameters\": [{\"default\": null, \"description\": \"Python command to execute in the notebook environment\", \"name\": \"command\", \"type\": \"str\"}], \"id\": 174}, {\"name\": \"csvtk_headers\", \"description\": \"Print headers of a CSV/TSV file.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7fbc17131260>\", \"id\": 237}, {\"name\": \"csvtk_cut\", \"description\": \"Select and arrange fields/columns.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7fbc17131620>\", \"id\": 243}, {\"name\": \"csvtk_join\", \"description\": \"Join files by selected fields.\", \"parameters\": {\"file1\": {\"type\": \"string\", \"description\": \"\"}, \"file2\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"left_join\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"outer_join\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"file1\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"file2\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"left_join\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"outer_join\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7fbc17131940>\", \"id\": 248}, {\"name\": \"csvtk_concat\", \"description\": \"Concatenate CSV/TSV files by rows.\", \"parameters\": {\"files\": {\"type\": \"array\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"files\", \"type\": \"array\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7fbc171319e0>\", \"id\": 249}, {\"name\": \"csvtk_rename\", \"description\": \"Rename column names with new names.\", \"parameters\": {\"in_file\": {\"type\": \"string\", \"description\": \"\"}, \"fields\": {\"type\": \"string\", \"description\": \"\"}, \"names\": {\"type\": \"string\", \"description\": \"\"}, \"tabs\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_header_row\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"out_file\": {\"type\": \"string\", \"description\": \"\", \"default\": \"-\"}}, \"required_parameters\": [{\"name\": \"in_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"fields\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"names\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"tabs\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_header_row\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"out_file\", \"type\": \"string\", \"description\": \"\", \"default\": \"-\"}], \"module\": \"mcp_servers.csvtk\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7fbc17131d00>\", \"id\": 254}, {\"name\": \"deseq2_differential_expression\", \"description\": \"Performs differential expression analysis using DESeq2.\", \"parameters\": {\"counts_path\": {\"type\": \"string\", \"description\": \"\"}, \"metadata_path\": {\"type\": \"string\", \"description\": \"\"}, \"design_formula\": {\"type\": \"string\", \"description\": \"\"}, \"output_results_path\": {\"type\": \"string\", \"description\": \"\"}, \"contrast_column\": {\"type\": \"string\", \"description\": \"\", \"default\": null}, \"reference_level\": {\"type\": \"string\", \"description\": \"\", \"default\": null}, \"treated_level\": {\"type\": \"string\", \"description\": \"\", \"default\": null}, \"alpha\": {\"type\": \"number\", \"description\": \"\", \"default\": 0.05}, \"lfc_threshold\": {\"type\": \"number\", \"description\": \"\", \"default\": 0.0}, \"test_type\": {\"type\": \"string\", \"description\": \"\", \"default\": \"Wald\"}, \"fit_type\": {\"type\": \"string\", \"description\": \"\", \"default\": \"parametric\"}, \"reduced_formula\": {\"type\": \"string\", \"description\": \"\", \"default\": null}, \"shrink_lfc\": {\"type\": \"boolean\", \"description\": \"\", \"default\": true}, \"shrink_type\": {\"type\": \"string\", \"description\": \"\", \"default\": \"apeglm\"}}, \"required_parameters\": [{\"name\": \"counts_path\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"metadata_path\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"design_formula\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"output_results_path\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"contrast_column\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"reference_level\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"treated_level\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"alpha\", \"type\": \"number\", \"description\": \"\", \"default\": 0.05}, {\"name\": \"lfc_threshold\", \"type\": \"number\", \"description\": \"\", \"default\": 0.0}, {\"name\": \"test_type\", \"type\": \"string\", \"description\": \"\", \"default\": \"Wald\"}, {\"name\": \"fit_type\", \"type\": \"string\", \"description\": \"\", \"default\": \"parametric\"}, {\"name\": \"reduced_formula\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"shrink_lfc\", \"type\": \"boolean\", \"description\": \"\", \"default\": true}, {\"name\": \"shrink_type\", \"type\": \"string\", \"description\": \"\", \"default\": \"apeglm\"}], \"module\": \"mcp_servers.bioconductor_deseq2\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7fbc16ad93a0>\", \"id\": 341}, {\"name\": \"deseq2_transform_counts\", \"description\": \"Transforms count data using Variance Stabilizing Transformation (VST) or Regularized Log (rlog).\", \"parameters\": {\"counts_path\": {\"type\": \"string\", \"description\": \"\"}, \"metadata_path\": {\"type\": \"string\", \"description\": \"\"}, \"design_formula\": {\"type\": \"string\", \"description\": \"\"}, \"output_path\": {\"type\": \"string\", \"description\": \"\"}, \"method\": {\"type\": \"string\", \"description\": \"\", \"default\": \"vst\"}, \"blind\": {\"type\": \"boolean\", \"description\": \"\", \"default\": true}}, \"required_parameters\": [{\"name\": \"counts_path\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"metadata_path\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"design_formula\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"output_path\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"method\", \"type\": \"string\", \"description\": \"\", \"default\": \"vst\"}, {\"name\": \"blind\", \"type\": \"boolean\", \"description\": \"\", \"default\": true}], \"module\": \"mcp_servers.bioconductor_deseq2\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7fbc16ad9440>\", \"id\": 342}, {\"name\": \"deseq2_get_normalized_counts\", \"description\": \"Calculates size factors and returns normalized counts.\", \"parameters\": {\"counts_path\": {\"type\": \"string\", \"description\": \"\"}, \"metadata_path\": {\"type\": \"string\", \"description\": \"\"}, \"design_formula\": {\"type\": \"string\", \"description\": \"\"}, \"output_path\": {\"type\": \"string\", \"description\": \"\"}, \"normalization_type\": {\"type\": \"string\", \"description\": \"\", \"default\": \"ratio\"}}, \"required_parameters\": [{\"name\": \"counts_path\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"metadata_path\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"design_formula\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"output_path\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"normalization_type\", \"type\": \"string\", \"description\": \"\", \"default\": \"ratio\"}], \"module\": \"mcp_servers.bioconductor_deseq2\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7fbc16ad94e0>\", \"id\": 343}, {\"name\": \"enrich_kegg\", \"description\": \"Performs KEGG pathway over-representation analysis using clusterProfiler::enrichKEGG.\", \"parameters\": {\"gene_file\": {\"type\": \"string\", \"description\": \"\"}, \"organism\": {\"type\": \"string\", \"description\": \"\"}, \"output_prefix\": {\"type\": \"string\", \"description\": \"\"}, \"keyType\": {\"type\": \"string\", \"description\": \"\", \"default\": \"kegg\"}, \"pvalue_cutoff\": {\"type\": \"number\", \"description\": \"\", \"default\": 0.05}, \"qvalue_cutoff\": {\"type\": \"number\", \"description\": \"\", \"default\": 0.2}, \"p_adjust_method\": {\"type\": \"string\", \"description\": \"\", \"default\": \"BH\"}, \"universe_file\": {\"type\": \"string\", \"description\": \"\", \"default\": null}, \"min_gs_size\": {\"type\": \"number\", \"description\": \"\", \"default\": 10}, \"max_gs_size\": {\"type\": \"number\", \"description\": \"\", \"default\": 500}}, \"required_parameters\": [{\"name\": \"gene_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"organism\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"output_prefix\", \"type\": \"string\", \"description\": \"\", \"default\": null}], \"optional_parameters\": [{\"name\": \"keyType\", \"type\": \"string\", \"description\": \"\", \"default\": \"kegg\"}, {\"name\": \"pvalue_cutoff\", \"type\": \"number\", \"description\": \"\", \"default\": 0.05}, {\"name\": \"qvalue_cutoff\", \"type\": \"number\", \"description\": \"\", \"default\": 0.2}, {\"name\": \"p_adjust_method\", \"type\": \"string\", \"description\": \"\", \"default\": \"BH\"}, {\"name\": \"universe_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"min_gs_size\", \"type\": \"number\", \"description\": \"\", \"default\": 10}, {\"name\": \"max_gs_size\", \"type\": \"number\", \"description\": \"\", \"default\": 500}], \"module\": \"mcp_servers.bioconductor_clusterprofiler\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7fbc16ad98a0>\", \"id\": 349}, {\"name\": \"rscript\", \"description\": \"Executes an R script or R expressions using the Rscript command-line tool.\", \"parameters\": {\"script_file\": {\"type\": \"string\", \"description\": \"\", \"default\": null}, \"expressions\": {\"type\": \"array\", \"description\": \"\", \"default\": null}, \"script_args\": {\"type\": \"array\", \"description\": \"\", \"default\": null}, \"verbose\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"default_packages\": {\"type\": \"string\", \"description\": \"\", \"default\": null}, \"vanilla\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"save\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_environ\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_site_file\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"no_init_file\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}, \"restore\": {\"type\": \"boolean\", \"description\": \"\", \"default\": false}}, \"required_parameters\": [], \"optional_parameters\": [{\"name\": \"script_file\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"expressions\", \"type\": \"array\", \"description\": \"\", \"default\": null}, {\"name\": \"script_args\", \"type\": \"array\", \"description\": \"\", \"default\": null}, {\"name\": \"verbose\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"default_packages\", \"type\": \"string\", \"description\": \"\", \"default\": null}, {\"name\": \"vanilla\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"save\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_environ\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_site_file\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"no_init_file\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}, {\"name\": \"restore\", \"type\": \"boolean\", \"description\": \"\", \"default\": false}], \"module\": \"mcp_servers.bioconductor_annotate\", \"fn\": \"<function A1.add_mcp.<locals>.make_mcp_wrapper.<locals>.sync_tool_wrapper at 0x7fbc18ce49a0>\", \"id\": 631}], \"data_lake\": [], \"libraries\": [\"gseapy\", \"pandas\", \"numpy\", \"scipy\", \"matplotlib\", \"dplyr\", \"readr\", \"DESeq2\", \"clusterProfiler\"], \"know_how\": []}}",
|
| 6 |
+
"planning_latency_seconds": 27.729597624391317,
|
| 7 |
+
"total_runtime_seconds": 906.5953246429563,
|
| 8 |
+
"selected_resources": {
|
| 9 |
+
"tools": [
|
| 10 |
+
{
|
| 11 |
+
"name": "run_python_repl",
|
| 12 |
+
"module": "biomni.tool.support_tools",
|
| 13 |
+
"description": "Executes the provided Python command in the notebook environment and returns the output."
|
| 14 |
+
},
|
| 15 |
+
{
|
| 16 |
+
"name": "csvtk_headers",
|
| 17 |
+
"module": "mcp_servers.csvtk",
|
| 18 |
+
"description": "Print headers of a CSV/TSV file."
|
| 19 |
+
},
|
| 20 |
+
{
|
| 21 |
+
"name": "csvtk_cut",
|
| 22 |
+
"module": "mcp_servers.csvtk",
|
| 23 |
+
"description": "Select and arrange fields/columns."
|
| 24 |
+
},
|
| 25 |
+
{
|
| 26 |
+
"name": "csvtk_join",
|
| 27 |
+
"module": "mcp_servers.csvtk",
|
| 28 |
+
"description": "Join files by selected fields."
|
| 29 |
+
},
|
| 30 |
+
{
|
| 31 |
+
"name": "csvtk_concat",
|
| 32 |
+
"module": "mcp_servers.csvtk",
|
| 33 |
+
"description": "Concatenate CSV/TSV files by rows."
|
| 34 |
+
},
|
| 35 |
+
{
|
| 36 |
+
"name": "csvtk_rename",
|
| 37 |
+
"module": "mcp_servers.csvtk",
|
| 38 |
+
"description": "Rename column names with new names."
|
| 39 |
+
},
|
| 40 |
+
{
|
| 41 |
+
"name": "deseq2_differential_expression",
|
| 42 |
+
"module": "mcp_servers.bioconductor_deseq2",
|
| 43 |
+
"description": "Performs differential expression analysis using DESeq2."
|
| 44 |
+
},
|
| 45 |
+
{
|
| 46 |
+
"name": "deseq2_transform_counts",
|
| 47 |
+
"module": "mcp_servers.bioconductor_deseq2",
|
| 48 |
+
"description": "Transforms count data using Variance Stabilizing Transformation (VST) or Regularized Log (rlog)."
|
| 49 |
+
},
|
| 50 |
+
{
|
| 51 |
+
"name": "deseq2_get_normalized_counts",
|
| 52 |
+
"module": "mcp_servers.bioconductor_deseq2",
|
| 53 |
+
"description": "Calculates size factors and returns normalized counts."
|
| 54 |
+
},
|
| 55 |
+
{
|
| 56 |
+
"name": "enrich_kegg",
|
| 57 |
+
"module": "mcp_servers.bioconductor_clusterprofiler",
|
| 58 |
+
"description": "Performs KEGG pathway over-representation analysis using clusterProfiler::enrichKEGG."
|
| 59 |
+
},
|
| 60 |
+
{
|
| 61 |
+
"name": "rscript",
|
| 62 |
+
"module": "mcp_servers.bioconductor_annotate",
|
| 63 |
+
"description": "Executes an R script or R expressions using the Rscript command-line tool."
|
| 64 |
+
}
|
| 65 |
+
],
|
| 66 |
+
"data_lake": [],
|
| 67 |
+
"libraries": [
|
| 68 |
+
{
|
| 69 |
+
"name": "gseapy",
|
| 70 |
+
"description": "[Python Package] A Python wrapper for Gene Set Enrichment Analysis (GSEA) and visualization."
|
| 71 |
+
},
|
| 72 |
+
{
|
| 73 |
+
"name": "pandas",
|
| 74 |
+
"description": "[Python Package] A fast, powerful, and flexible data analysis and manipulation library for Python."
|
| 75 |
+
},
|
| 76 |
+
{
|
| 77 |
+
"name": "numpy",
|
| 78 |
+
"description": "[Python Package] The fundamental package for scientific computing with Python, providing support for arrays, matrices, and mathematical functions."
|
| 79 |
+
},
|
| 80 |
+
{
|
| 81 |
+
"name": "scipy",
|
| 82 |
+
"description": "[Python Package] A Python library for scientific and technical computing, including modules for optimization, linear algebra, integration, and statistics."
|
| 83 |
+
},
|
| 84 |
+
{
|
| 85 |
+
"name": "matplotlib",
|
| 86 |
+
"description": "[Python Package] A comprehensive library for creating static, animated, and interactive visualizations in Python."
|
| 87 |
+
},
|
| 88 |
+
{
|
| 89 |
+
"name": "dplyr",
|
| 90 |
+
"description": "[R Package] A grammar of data manipulation, providing a consistent set of verbs that help you solve the most common data manipulation challenges. Use with subprocess."
|
| 91 |
+
},
|
| 92 |
+
{
|
| 93 |
+
"name": "readr",
|
| 94 |
+
"description": "[R Package] A fast and friendly way to read rectangular data like CSV, TSV, and FWF. Use with subprocess.run(['Rscript', '-e', 'library(readr); ...'])."
|
| 95 |
+
},
|
| 96 |
+
{
|
| 97 |
+
"name": "DESeq2",
|
| 98 |
+
"description": "[R Package] Differential gene expression analysis based on the negative binomial distribution. Use with subprocess.run(['Rscript', '-e', 'library(DESeq2); ...'])."
|
| 99 |
+
},
|
| 100 |
+
{
|
| 101 |
+
"name": "clusterProfiler",
|
| 102 |
+
"description": "[R Package] A package for statistical analysis and visualization of functional profiles for genes and gene clusters. Use with subprocess calls."
|
| 103 |
+
}
|
| 104 |
+
],
|
| 105 |
+
"know_how": []
|
| 106 |
+
},
|
| 107 |
+
"selected_resource_names": {
|
| 108 |
+
"tools": [
|
| 109 |
+
"run_python_repl",
|
| 110 |
+
"csvtk_headers",
|
| 111 |
+
"csvtk_cut",
|
| 112 |
+
"csvtk_join",
|
| 113 |
+
"csvtk_concat",
|
| 114 |
+
"csvtk_rename",
|
| 115 |
+
"deseq2_differential_expression",
|
| 116 |
+
"deseq2_transform_counts",
|
| 117 |
+
"deseq2_get_normalized_counts",
|
| 118 |
+
"enrich_kegg",
|
| 119 |
+
"rscript"
|
| 120 |
+
],
|
| 121 |
+
"data_lake": [],
|
| 122 |
+
"libraries": [
|
| 123 |
+
"gseapy",
|
| 124 |
+
"pandas",
|
| 125 |
+
"numpy",
|
| 126 |
+
"scipy",
|
| 127 |
+
"matplotlib",
|
| 128 |
+
"dplyr",
|
| 129 |
+
"readr",
|
| 130 |
+
"DESeq2",
|
| 131 |
+
"clusterProfiler"
|
| 132 |
+
],
|
| 133 |
+
"know_how": []
|
| 134 |
+
},
|
| 135 |
+
"registered_tool_count": 1226,
|
| 136 |
+
"registered_tool_names": [
|
| 137 |
+
"fetch_supplementary_info_from_doi",
|
| 138 |
+
"query_arxiv",
|
| 139 |
+
"query_scholar",
|
| 140 |
+
"query_pubmed",
|
| 141 |
+
"search_google",
|
| 142 |
+
"extract_url_content",
|
| 143 |
+
"extract_pdf_content",
|
| 144 |
+
"advanced_web_search_claude",
|
| 145 |
+
"analyze_circular_dichroism_spectra",
|
| 146 |
+
"analyze_rna_secondary_structure_features",
|
| 147 |
+
"analyze_protease_kinetics",
|
| 148 |
+
"analyze_enzyme_kinetics_assay",
|
| 149 |
+
"analyze_itc_binding_thermodynamics",
|
| 150 |
+
"analyze_protein_conservation",
|
| 151 |
+
"split_modalities",
|
| 152 |
+
"prepare_input_for_nnunet",
|
| 153 |
+
"segment_with_nn_unet",
|
| 154 |
+
"create_segmentation_visualization",
|
| 155 |
+
"quick_rigid_registration",
|
| 156 |
+
"quick_affine_registration",
|
| 157 |
+
"quick_deformable_registration",
|
| 158 |
+
"batch_register_images",
|
| 159 |
+
"calculate_similarity_metrics",
|
| 160 |
+
"create_registration_visualization",
|
| 161 |
+
"analyze_cell_migration_metrics",
|
| 162 |
+
"perform_crispr_cas9_genome_editing",
|
| 163 |
+
"analyze_calcium_imaging_data",
|
| 164 |
+
"analyze_in_vitro_drug_release_kinetics",
|
| 165 |
+
"analyze_myofiber_morphology",
|
| 166 |
+
"decode_behavior_from_neural_trajectories",
|
| 167 |
+
"simulate_whole_cell_ode_model",
|
| 168 |
+
"predict_protein_disorder_regions",
|
| 169 |
+
"analyze_cell_morphology_and_cytoskeleton",
|
| 170 |
+
"analyze_tissue_deformation_flow",
|
| 171 |
+
"find_n_glycosylation_motifs",
|
| 172 |
+
"predict_o_glycosylation_hotspots",
|
| 173 |
+
"list_glycoengineering_resources",
|
| 174 |
+
"analyze_ddr_network_in_cancer",
|
| 175 |
+
"analyze_cell_senescence_and_apoptosis",
|
| 176 |
+
"detect_and_annotate_somatic_mutations",
|
| 177 |
+
"detect_and_characterize_structural_variations",
|
| 178 |
+
"perform_gene_expression_nmf_analysis",
|
| 179 |
+
"analyze_copy_number_purity_ploidy_and_focal_events",
|
| 180 |
+
"quantify_cell_cycle_phases_from_microscopy",
|
| 181 |
+
"quantify_and_cluster_cell_motility",
|
| 182 |
+
"perform_facs_cell_sorting",
|
| 183 |
+
"analyze_flow_cytometry_immunophenotyping",
|
| 184 |
+
"analyze_mitochondrial_morphology_and_potential",
|
| 185 |
+
"annotate_open_reading_frames",
|
| 186 |
+
"annotate_plasmid",
|
| 187 |
+
"get_gene_coding_sequence",
|
| 188 |
+
"get_plasmid_sequence",
|
| 189 |
+
"align_sequences",
|
| 190 |
+
"pcr_simple",
|
| 191 |
+
"digest_sequence",
|
| 192 |
+
"find_restriction_sites",
|
| 193 |
+
"find_restriction_enzymes",
|
| 194 |
+
"find_sequence_mutations",
|
| 195 |
+
"design_knockout_sgrna",
|
| 196 |
+
"get_oligo_annealing_protocol",
|
| 197 |
+
"get_golden_gate_assembly_protocol",
|
| 198 |
+
"get_bacterial_transformation_protocol",
|
| 199 |
+
"design_primer",
|
| 200 |
+
"design_verification_primers",
|
| 201 |
+
"design_golden_gate_oligos",
|
| 202 |
+
"golden_gate_assembly",
|
| 203 |
+
"liftover_coordinates",
|
| 204 |
+
"bayesian_finemapping_with_deep_vi",
|
| 205 |
+
"analyze_cas9_mutation_outcomes",
|
| 206 |
+
"analyze_crispr_genome_editing",
|
| 207 |
+
"simulate_demographic_history",
|
| 208 |
+
"identify_transcription_factor_binding_sites",
|
| 209 |
+
"fit_genomic_prediction_model",
|
| 210 |
+
"perform_pcr_and_gel_electrophoresis",
|
| 211 |
+
"analyze_protein_phylogeny",
|
| 212 |
+
"annotate_celltype_scRNA",
|
| 213 |
+
"annotate_celltype_with_panhumanpy",
|
| 214 |
+
"create_scvi_embeddings_scRNA",
|
| 215 |
+
"create_harmony_embeddings_scRNA",
|
| 216 |
+
"get_uce_embeddings_scRNA",
|
| 217 |
+
"map_to_ima_interpret_scRNA",
|
| 218 |
+
"get_rna_seq_archs4",
|
| 219 |
+
"get_gene_set_enrichment_analysis_supported_database_list",
|
| 220 |
+
"gene_set_enrichment_analysis",
|
| 221 |
+
"analyze_chromatin_interactions",
|
| 222 |
+
"analyze_comparative_genomics_and_haplotypes",
|
| 223 |
+
"perform_chipseq_peak_calling_with_macs2",
|
| 224 |
+
"find_enriched_motifs_with_homer",
|
| 225 |
+
"analyze_genomic_region_overlap",
|
| 226 |
+
"unsupervised_celltype_transfer_between_scRNA_datasets",
|
| 227 |
+
"generate_embeddings_with_state",
|
| 228 |
+
"interspecies_gene_conversion",
|
| 229 |
+
"generate_gene_embeddings_with_ESM_models",
|
| 230 |
+
"generate_transcriptformer_embeddings",
|
| 231 |
+
"analyze_atac_seq_differential_accessibility",
|
| 232 |
+
"analyze_bacterial_growth_curve",
|
| 233 |
+
"isolate_purify_immune_cells",
|
| 234 |
+
"estimate_cell_cycle_phase_durations",
|
| 235 |
+
"track_immune_cells_under_flow",
|
| 236 |
+
"analyze_cfse_cell_proliferation",
|
| 237 |
+
"analyze_cytokine_production_in_cd4_tcells",
|
| 238 |
+
"analyze_ebv_antibody_titers",
|
| 239 |
+
"analyze_cns_lesion_histology",
|
| 240 |
+
"analyze_immunohistochemistry_image",
|
| 241 |
+
"optimize_anaerobic_digestion_process",
|
| 242 |
+
"analyze_arsenic_speciation_hplc_icpms",
|
| 243 |
+
"count_bacterial_colonies",
|
| 244 |
+
"annotate_bacterial_genome",
|
| 245 |
+
"enumerate_bacterial_cfu_by_serial_dilution",
|
| 246 |
+
"model_bacterial_growth_dynamics",
|
| 247 |
+
"quantify_biofilm_biomass_crystal_violet",
|
| 248 |
+
"segment_and_analyze_microbial_cells",
|
| 249 |
+
"segment_cells_with_deep_learning",
|
| 250 |
+
"simulate_generalized_lotka_volterra_dynamics",
|
| 251 |
+
"predict_rna_secondary_structure",
|
| 252 |
+
"simulate_microbial_population_dynamics",
|
| 253 |
+
"analyze_aortic_diameter_and_geometry",
|
| 254 |
+
"analyze_atp_luminescence_assay",
|
| 255 |
+
"analyze_thrombus_histology",
|
| 256 |
+
"analyze_intracellular_calcium_with_rhod2",
|
| 257 |
+
"quantify_corneal_nerve_fibers",
|
| 258 |
+
"segment_and_quantify_cells_in_multiplexed_images",
|
| 259 |
+
"analyze_bone_microct_morphometry",
|
| 260 |
+
"run_diffdock_with_smiles",
|
| 261 |
+
"docking_autodock_vina",
|
| 262 |
+
"run_autosite",
|
| 263 |
+
"retrieve_topk_repurposing_drugs_from_disease_txgnn",
|
| 264 |
+
"predict_admet_properties",
|
| 265 |
+
"predict_binding_affinity_protein_1d_sequence",
|
| 266 |
+
"analyze_accelerated_stability_of_pharmaceutical_formulations",
|
| 267 |
+
"run_3d_chondrogenic_aggregate_assay",
|
| 268 |
+
"grade_adverse_events_using_vcog_ctcae",
|
| 269 |
+
"analyze_radiolabeled_antibody_biodistribution",
|
| 270 |
+
"estimate_alpha_particle_radiotherapy_dosimetry",
|
| 271 |
+
"perform_mwas_cyp2c19_metabolizer_status",
|
| 272 |
+
"calculate_physicochemical_properties",
|
| 273 |
+
"analyze_xenograft_tumor_growth_inhibition",
|
| 274 |
+
"analyze_pixel_distribution",
|
| 275 |
+
"find_roi_from_image",
|
| 276 |
+
"analyze_western_blot",
|
| 277 |
+
"query_drug_interactions",
|
| 278 |
+
"check_drug_combination_safety",
|
| 279 |
+
"analyze_interaction_mechanisms",
|
| 280 |
+
"find_alternative_drugs_ddinter",
|
| 281 |
+
"query_fda_adverse_events",
|
| 282 |
+
"get_fda_drug_label_info",
|
| 283 |
+
"check_fda_drug_recalls",
|
| 284 |
+
"analyze_fda_safety_signals",
|
| 285 |
+
"reconstruct_3d_face_from_mri",
|
| 286 |
+
"analyze_abr_waveform_p1_metrics",
|
| 287 |
+
"analyze_ciliary_beat_frequency",
|
| 288 |
+
"analyze_protein_colocalization",
|
| 289 |
+
"perform_cosinor_analysis",
|
| 290 |
+
"calculate_brain_adc_map",
|
| 291 |
+
"analyze_endolysosomal_calcium_dynamics",
|
| 292 |
+
"analyze_fatty_acid_composition_by_gc",
|
| 293 |
+
"analyze_hemodynamic_data",
|
| 294 |
+
"simulate_thyroid_hormone_pharmacokinetics",
|
| 295 |
+
"quantify_amyloid_beta_plaques",
|
| 296 |
+
"engineer_bacterial_genome_for_therapeutic_delivery",
|
| 297 |
+
"analyze_bacterial_growth_rate",
|
| 298 |
+
"analyze_barcode_sequencing_data",
|
| 299 |
+
"analyze_bifurcation_diagram",
|
| 300 |
+
"create_biochemical_network_sbml_model",
|
| 301 |
+
"optimize_codons_for_heterologous_expression",
|
| 302 |
+
"simulate_gene_circuit_with_growth_feedback",
|
| 303 |
+
"identify_fas_functional_domains",
|
| 304 |
+
"perform_flux_balance_analysis",
|
| 305 |
+
"model_protein_dimerization_network",
|
| 306 |
+
"simulate_metabolic_network_perturbation",
|
| 307 |
+
"simulate_protein_signaling_network",
|
| 308 |
+
"compare_protein_structures",
|
| 309 |
+
"simulate_renin_angiotensin_system_dynamics",
|
| 310 |
+
"query_chatnt",
|
| 311 |
+
"run_python_repl",
|
| 312 |
+
"read_function_source_code",
|
| 313 |
+
"download_synapse_data",
|
| 314 |
+
"query_uniprot",
|
| 315 |
+
"query_alphafold",
|
| 316 |
+
"query_interpro",
|
| 317 |
+
"query_pdb",
|
| 318 |
+
"query_pdb_identifiers",
|
| 319 |
+
"query_kegg",
|
| 320 |
+
"query_stringdb",
|
| 321 |
+
"query_iucn",
|
| 322 |
+
"query_paleobiology",
|
| 323 |
+
"query_jaspar",
|
| 324 |
+
"query_worms",
|
| 325 |
+
"query_cbioportal",
|
| 326 |
+
"query_clinvar",
|
| 327 |
+
"query_geo",
|
| 328 |
+
"query_dbsnp",
|
| 329 |
+
"query_ucsc",
|
| 330 |
+
"query_ensembl",
|
| 331 |
+
"query_opentarget",
|
| 332 |
+
"query_monarch",
|
| 333 |
+
"query_openfda",
|
| 334 |
+
"query_gwas_catalog",
|
| 335 |
+
"query_gnomad",
|
| 336 |
+
"blast_sequence",
|
| 337 |
+
"query_reactome",
|
| 338 |
+
"query_regulomedb",
|
| 339 |
+
"query_pride",
|
| 340 |
+
"query_gtopdb",
|
| 341 |
+
"query_remap",
|
| 342 |
+
"query_mpd",
|
| 343 |
+
"query_emdb",
|
| 344 |
+
"query_synapse",
|
| 345 |
+
"query_pubchem",
|
| 346 |
+
"query_chembl",
|
| 347 |
+
"query_unichem",
|
| 348 |
+
"query_clinicaltrials",
|
| 349 |
+
"query_dailymed",
|
| 350 |
+
"query_quickgo",
|
| 351 |
+
"query_encode",
|
| 352 |
+
"region_to_ccre_screen",
|
| 353 |
+
"get_genes_near_ccre",
|
| 354 |
+
"test_pylabrobot_script",
|
| 355 |
+
"get_pylabrobot_documentation_liquid",
|
| 356 |
+
"get_pylabrobot_documentation_material",
|
| 357 |
+
"search_protocols",
|
| 358 |
+
"get_protocol_details",
|
| 359 |
+
"list_local_protocols",
|
| 360 |
+
"read_local_protocol",
|
| 361 |
+
"kallisto_index",
|
| 362 |
+
"kallisto_quant",
|
| 363 |
+
"kallisto_bus",
|
| 364 |
+
"kallisto_quant_tcc",
|
| 365 |
+
"kallisto_h5dump",
|
| 366 |
+
"kallisto_inspect",
|
| 367 |
+
"kallisto_version",
|
| 368 |
+
"kallisto_cite",
|
| 369 |
+
"kallisto_bus_list_technologies",
|
| 370 |
+
"kallisto_merge",
|
| 371 |
+
"kraken2_classify",
|
| 372 |
+
"kraken2_build_db",
|
| 373 |
+
"kraken2_inspect_db",
|
| 374 |
+
"csvtk_headers",
|
| 375 |
+
"csvtk_dim",
|
| 376 |
+
"csvtk_ncol",
|
| 377 |
+
"csvtk_nrow",
|
| 378 |
+
"csvtk_corr",
|
| 379 |
+
"csvtk_summary",
|
| 380 |
+
"csvtk_cut",
|
| 381 |
+
"csvtk_grep",
|
| 382 |
+
"csvtk_filter",
|
| 383 |
+
"csvtk_filter2",
|
| 384 |
+
"csvtk_sort",
|
| 385 |
+
"csvtk_join",
|
| 386 |
+
"csvtk_concat",
|
| 387 |
+
"csvtk_uniq",
|
| 388 |
+
"csvtk_freq",
|
| 389 |
+
"csvtk_mutate",
|
| 390 |
+
"csvtk_mutate2",
|
| 391 |
+
"csvtk_rename",
|
| 392 |
+
"csvtk_replace",
|
| 393 |
+
"csvtk_round",
|
| 394 |
+
"csvtk_transpose",
|
| 395 |
+
"csvtk_sep",
|
| 396 |
+
"csvtk_gather",
|
| 397 |
+
"csvtk_spread",
|
| 398 |
+
"csvtk_pretty",
|
| 399 |
+
"csvtk_csv2md",
|
| 400 |
+
"csvtk_csv2json",
|
| 401 |
+
"csvtk_xlsx2csv",
|
| 402 |
+
"csvtk_fix",
|
| 403 |
+
"csvtk_fix_quotes",
|
| 404 |
+
"csvtk_del_quotes",
|
| 405 |
+
"csvtk_head",
|
| 406 |
+
"csvtk_sample",
|
| 407 |
+
"csvtk_split",
|
| 408 |
+
"csvtk_comb",
|
| 409 |
+
"csvtk_fmtdate",
|
| 410 |
+
"csvtk_fold",
|
| 411 |
+
"csvtk_unfold",
|
| 412 |
+
"csvtk_plot",
|
| 413 |
+
"csvtk_version",
|
| 414 |
+
"megahit_assemble",
|
| 415 |
+
"megahit_core_contig2fastg",
|
| 416 |
+
"kaiju_classify",
|
| 417 |
+
"kaiju_makedb",
|
| 418 |
+
"kaiju_mkbwt",
|
| 419 |
+
"kaiju_mkfmi",
|
| 420 |
+
"kaiju_multi_classify",
|
| 421 |
+
"kaiju2krona",
|
| 422 |
+
"kaiju2table",
|
| 423 |
+
"kaiju_add_taxon_names",
|
| 424 |
+
"kaiju_merge_outputs",
|
| 425 |
+
"kaijux_search",
|
| 426 |
+
"kaijup_search",
|
| 427 |
+
"fastp_tool",
|
| 428 |
+
"spades_py",
|
| 429 |
+
"metaspades_py",
|
| 430 |
+
"rnaspades_py",
|
| 431 |
+
"plasmidspades_py",
|
| 432 |
+
"metaviralspades_py",
|
| 433 |
+
"coronaspades_py",
|
| 434 |
+
"biosyntheticspades_py",
|
| 435 |
+
"spades_test",
|
| 436 |
+
"spades_kmercount",
|
| 437 |
+
"spades_hammer",
|
| 438 |
+
"settings",
|
| 439 |
+
"scanpy_filter",
|
| 440 |
+
"scanpy_norm",
|
| 441 |
+
"scanpy_log1p",
|
| 442 |
+
"scanpy_hvg",
|
| 443 |
+
"scanpy_scale",
|
| 444 |
+
"scanpy_pca",
|
| 445 |
+
"scanpy_neighbors",
|
| 446 |
+
"scanpy_umap",
|
| 447 |
+
"scanpy_tsne",
|
| 448 |
+
"scanpy_diffexp",
|
| 449 |
+
"scanpy_louvain",
|
| 450 |
+
"scanpy_leiden",
|
| 451 |
+
"scanpy_paga",
|
| 452 |
+
"scanpy_cli_read",
|
| 453 |
+
"scanpy_cli_filter",
|
| 454 |
+
"scanpy_cli_norm",
|
| 455 |
+
"scanpy_cli_hvg",
|
| 456 |
+
"scanpy_cli_scale",
|
| 457 |
+
"scanpy_cli_regress",
|
| 458 |
+
"scanpy_cli_pca",
|
| 459 |
+
"scanpy_cli_neighbor",
|
| 460 |
+
"scanpy_cli_embed",
|
| 461 |
+
"scanpy_cli_cluster",
|
| 462 |
+
"scanpy_cli_diffexp",
|
| 463 |
+
"scanpy_cli_paga",
|
| 464 |
+
"scanpy_cli_dpt",
|
| 465 |
+
"scanpy_cli_integrate",
|
| 466 |
+
"scanpy_cli_multiplet",
|
| 467 |
+
"scanpy_cli_plot",
|
| 468 |
+
"seurat_read_10x",
|
| 469 |
+
"seurat_filter_cells",
|
| 470 |
+
"seurat_normalize_data",
|
| 471 |
+
"seurat_find_variable_features",
|
| 472 |
+
"seurat_scale_data",
|
| 473 |
+
"seurat_run_pca",
|
| 474 |
+
"seurat_find_neighbors",
|
| 475 |
+
"seurat_find_clusters",
|
| 476 |
+
"seurat_run_umap",
|
| 477 |
+
"seurat_find_markers",
|
| 478 |
+
"deseq2_differential_expression",
|
| 479 |
+
"deseq2_transform_counts",
|
| 480 |
+
"deseq2_get_normalized_counts",
|
| 481 |
+
"deseq2_plot_pca",
|
| 482 |
+
"run_edger_glm",
|
| 483 |
+
"run_edger_exact_test",
|
| 484 |
+
"limma_voom_differential_expression",
|
| 485 |
+
"enrich_go",
|
| 486 |
+
"enrich_kegg",
|
| 487 |
+
"gse_go",
|
| 488 |
+
"gse_kegg",
|
| 489 |
+
"compare_clusters_go",
|
| 490 |
+
"star_genome_generate",
|
| 491 |
+
"star_align_reads",
|
| 492 |
+
"star_lift_over",
|
| 493 |
+
"star_generic_command",
|
| 494 |
+
"hisat2_align",
|
| 495 |
+
"hisat2_build",
|
| 496 |
+
"hisat2_inspect",
|
| 497 |
+
"hisat2_extract_splice_sites",
|
| 498 |
+
"hisat2_extract_exons",
|
| 499 |
+
"hisat2_simulate_reads",
|
| 500 |
+
"subread_buildindex",
|
| 501 |
+
"subread_align",
|
| 502 |
+
"subjunc",
|
| 503 |
+
"feature_counts",
|
| 504 |
+
"sublong",
|
| 505 |
+
"exact_snp",
|
| 506 |
+
"flatten_gtf",
|
| 507 |
+
"remove_dup",
|
| 508 |
+
"bcftools_annotate",
|
| 509 |
+
"bcftools_call",
|
| 510 |
+
"bcftools_concat",
|
| 511 |
+
"bcftools_consensus",
|
| 512 |
+
"bcftools_filter",
|
| 513 |
+
"bcftools_index",
|
| 514 |
+
"bcftools_isec",
|
| 515 |
+
"bcftools_merge",
|
| 516 |
+
"bcftools_mpileup",
|
| 517 |
+
"bcftools_norm",
|
| 518 |
+
"bcftools_query",
|
| 519 |
+
"bcftools_reheader",
|
| 520 |
+
"bcftools_sort",
|
| 521 |
+
"bcftools_stats",
|
| 522 |
+
"bcftools_view",
|
| 523 |
+
"bwa_index",
|
| 524 |
+
"bwa_mem",
|
| 525 |
+
"bwa_aln",
|
| 526 |
+
"bwa_samse",
|
| 527 |
+
"bwa_sampe",
|
| 528 |
+
"bwa_fastmap",
|
| 529 |
+
"bwa_shm",
|
| 530 |
+
"bwa_fa2pac",
|
| 531 |
+
"bwa_pac2bwt",
|
| 532 |
+
"bwa_bwtupdate",
|
| 533 |
+
"bwa_bwt2sa",
|
| 534 |
+
"gatk4_list_tools",
|
| 535 |
+
"gatk4_tool_help",
|
| 536 |
+
"gatk4_haplotype_caller",
|
| 537 |
+
"gatk4_mutect2",
|
| 538 |
+
"gatk4_mark_duplicates",
|
| 539 |
+
"gatk4_base_recalibrator",
|
| 540 |
+
"gatk4_apply_bqsr",
|
| 541 |
+
"gatk4_print_reads",
|
| 542 |
+
"gatk4_run_spark_tool",
|
| 543 |
+
"gatk4_generic_tool_runner",
|
| 544 |
+
"gatk_haplotype_caller",
|
| 545 |
+
"gatk_mutect2",
|
| 546 |
+
"gatk_base_recalibrator",
|
| 547 |
+
"gatk_apply_bqsr",
|
| 548 |
+
"gatk_mark_duplicates",
|
| 549 |
+
"gatk_genotype_gvcfs",
|
| 550 |
+
"gatk_variant_filtration",
|
| 551 |
+
"gatk_select_variants",
|
| 552 |
+
"gatk_combine_gvcfs",
|
| 553 |
+
"gatk_get_pileup_summaries",
|
| 554 |
+
"gatk_calculate_contamination",
|
| 555 |
+
"gatk_filter_mutect_calls",
|
| 556 |
+
"gatk_sort_sam",
|
| 557 |
+
"gatk_validate_sam_file",
|
| 558 |
+
"snpeff_ann",
|
| 559 |
+
"snpeff_download",
|
| 560 |
+
"snpeff_databases",
|
| 561 |
+
"snpeff_build",
|
| 562 |
+
"snpeff_dump",
|
| 563 |
+
"snpeff_show",
|
| 564 |
+
"freebayes_call_variants",
|
| 565 |
+
"run_orthofinder",
|
| 566 |
+
"run_perl_script",
|
| 567 |
+
"run_perl_oneliner",
|
| 568 |
+
"check_perl_syntax",
|
| 569 |
+
"get_perl_version",
|
| 570 |
+
"get_perl_config",
|
| 571 |
+
"blastall",
|
| 572 |
+
"formatdb",
|
| 573 |
+
"makedb",
|
| 574 |
+
"prepdb",
|
| 575 |
+
"blastp",
|
| 576 |
+
"blastx",
|
| 577 |
+
"cluster",
|
| 578 |
+
"linclust",
|
| 579 |
+
"realign",
|
| 580 |
+
"recluster",
|
| 581 |
+
"reassign",
|
| 582 |
+
"view",
|
| 583 |
+
"merge_daa",
|
| 584 |
+
"version",
|
| 585 |
+
"getseq",
|
| 586 |
+
"dbinfo",
|
| 587 |
+
"test",
|
| 588 |
+
"makeidx",
|
| 589 |
+
"greedy_vertex_cover",
|
| 590 |
+
"gffread_tool",
|
| 591 |
+
"seqkit_stats",
|
| 592 |
+
"seqkit_seq",
|
| 593 |
+
"seqkit_grep",
|
| 594 |
+
"seqkit_subseq",
|
| 595 |
+
"seqkit_fq2fa",
|
| 596 |
+
"seqkit_fx2tab",
|
| 597 |
+
"seqkit_tab2fx",
|
| 598 |
+
"seqkit_translate",
|
| 599 |
+
"seqkit_rmdup",
|
| 600 |
+
"seqkit_sample",
|
| 601 |
+
"seqkit_sort",
|
| 602 |
+
"seqkit_split2",
|
| 603 |
+
"seqkit_locate",
|
| 604 |
+
"seqkit_replace",
|
| 605 |
+
"seqkit_faidx",
|
| 606 |
+
"seqkit_sliding",
|
| 607 |
+
"seqkit_common",
|
| 608 |
+
"seqkit_duplicate",
|
| 609 |
+
"seqkit_head",
|
| 610 |
+
"seqkit_pair",
|
| 611 |
+
"seqkit_mutate",
|
| 612 |
+
"seqkit_sum",
|
| 613 |
+
"seqkit_bam",
|
| 614 |
+
"seqkit_sana",
|
| 615 |
+
"seqkit_shuffle",
|
| 616 |
+
"seqkit_convert",
|
| 617 |
+
"seqkit_version",
|
| 618 |
+
"multiqc_run",
|
| 619 |
+
"multiqc_config",
|
| 620 |
+
"multiqc_plugin_list",
|
| 621 |
+
"multiqc_plugin_search",
|
| 622 |
+
"multiqc_plugin_install",
|
| 623 |
+
"multiqc_plugin_uninstall",
|
| 624 |
+
"multiqc_upgrade",
|
| 625 |
+
"multiqc_example",
|
| 626 |
+
"fastqc",
|
| 627 |
+
"trimmomatic_pe",
|
| 628 |
+
"trimmomatic_se",
|
| 629 |
+
"abnumber",
|
| 630 |
+
"abricate_run",
|
| 631 |
+
"abricate_list_databases",
|
| 632 |
+
"abricate_check_databases",
|
| 633 |
+
"abricate_setup_databases",
|
| 634 |
+
"abricate_get_version",
|
| 635 |
+
"abricate_get_citation",
|
| 636 |
+
"abundancebin",
|
| 637 |
+
"run_perl",
|
| 638 |
+
"perl_version",
|
| 639 |
+
"perl_config",
|
| 640 |
+
"adapter_removal",
|
| 641 |
+
"adapter_removal_identify_adapters",
|
| 642 |
+
"adapter_removal_demultiplex",
|
| 643 |
+
"alfred_stats",
|
| 644 |
+
"alfred_count",
|
| 645 |
+
"alfred_annotate",
|
| 646 |
+
"alfred_qc",
|
| 647 |
+
"alfred_merge",
|
| 648 |
+
"alfred_track",
|
| 649 |
+
"alfred_motif",
|
| 650 |
+
"export_scanpy",
|
| 651 |
+
"import_scanpy",
|
| 652 |
+
"anansnake_config",
|
| 653 |
+
"run_anansnake",
|
| 654 |
+
"run_anarci",
|
| 655 |
+
"list_anarci_species",
|
| 656 |
+
"get_anarci_version",
|
| 657 |
+
"aragorn",
|
| 658 |
+
"aria2_download",
|
| 659 |
+
"aria2_torrent",
|
| 660 |
+
"aria2_metalink",
|
| 661 |
+
"aria2_batch_download",
|
| 662 |
+
"aria2_rpc_server",
|
| 663 |
+
"pubmlstget",
|
| 664 |
+
"getref",
|
| 665 |
+
"prepareref",
|
| 666 |
+
"run",
|
| 667 |
+
"summary",
|
| 668 |
+
"version",
|
| 669 |
+
"test",
|
| 670 |
+
"run_arriba",
|
| 671 |
+
"draw_fusions",
|
| 672 |
+
"art_illumina",
|
| 673 |
+
"art_454",
|
| 674 |
+
"art_solid",
|
| 675 |
+
"art_profiler_illumina",
|
| 676 |
+
"arvados_cwl_runner",
|
| 677 |
+
"arvados_cwl_validate",
|
| 678 |
+
"arvados_cwl_create_workflow",
|
| 679 |
+
"arvados_cwl_update_workflow",
|
| 680 |
+
"arvados_cwl_create_template",
|
| 681 |
+
"arv_get",
|
| 682 |
+
"arv_put",
|
| 683 |
+
"arv_ls",
|
| 684 |
+
"arv_copy",
|
| 685 |
+
"arv_tag",
|
| 686 |
+
"atropos_trim",
|
| 687 |
+
"augustus",
|
| 688 |
+
"view",
|
| 689 |
+
"build",
|
| 690 |
+
"export_v1",
|
| 691 |
+
"export_v2",
|
| 692 |
+
"develop",
|
| 693 |
+
"version",
|
| 694 |
+
"bactopia_run",
|
| 695 |
+
"bactopia_prepare",
|
| 696 |
+
"bactopia_search",
|
| 697 |
+
"bactopia_datasets",
|
| 698 |
+
"bactopia_tool",
|
| 699 |
+
"convert",
|
| 700 |
+
"count",
|
| 701 |
+
"coverage",
|
| 702 |
+
"filter_bam",
|
| 703 |
+
"header",
|
| 704 |
+
"index",
|
| 705 |
+
"merge",
|
| 706 |
+
"random",
|
| 707 |
+
"resolve",
|
| 708 |
+
"revert",
|
| 709 |
+
"sort",
|
| 710 |
+
"split",
|
| 711 |
+
"stats",
|
| 712 |
+
"perl",
|
| 713 |
+
"bbmap",
|
| 714 |
+
"gff_to_bed",
|
| 715 |
+
"gff_filter_by_attribute",
|
| 716 |
+
"gff_filter_by_type",
|
| 717 |
+
"gff_stats",
|
| 718 |
+
"bcbio_nextgen_run",
|
| 719 |
+
"bcbio_nextgen_template",
|
| 720 |
+
"bcbio_nextgen_upgrade",
|
| 721 |
+
"bcbio_nextgen_install",
|
| 722 |
+
"bcbio_nextgen_version",
|
| 723 |
+
"bedops_complement",
|
| 724 |
+
"bedops_difference",
|
| 725 |
+
"bedops_element_of",
|
| 726 |
+
"bedops_intersect",
|
| 727 |
+
"bedops_merge",
|
| 728 |
+
"bedops_not_element_of",
|
| 729 |
+
"bedops_partition",
|
| 730 |
+
"bedops_symmdiff",
|
| 731 |
+
"bedops_everything",
|
| 732 |
+
"bedops_chop",
|
| 733 |
+
"intersect",
|
| 734 |
+
"merge",
|
| 735 |
+
"subtract",
|
| 736 |
+
"slop",
|
| 737 |
+
"getfasta",
|
| 738 |
+
"sort",
|
| 739 |
+
"coverage",
|
| 740 |
+
"genomecov",
|
| 741 |
+
"bin2cell_prepare_bins",
|
| 742 |
+
"bin2cell_run_stardist",
|
| 743 |
+
"bin2cell_extract_cells",
|
| 744 |
+
"bin2cell_visualize_segmentation",
|
| 745 |
+
"bioawk",
|
| 746 |
+
"bamsort",
|
| 747 |
+
"bammarkduplicates",
|
| 748 |
+
"bamsormadup",
|
| 749 |
+
"bamtofastq",
|
| 750 |
+
"bamcollate2",
|
| 751 |
+
"bamadapterclip",
|
| 752 |
+
"bamreset",
|
| 753 |
+
"bamchecksort",
|
| 754 |
+
"bamrecompress",
|
| 755 |
+
"bamfilterrg",
|
| 756 |
+
"bamfillquery",
|
| 757 |
+
"run_affy_analysis",
|
| 758 |
+
"affyio_read_celfile_header",
|
| 759 |
+
"affyio_read_celfile",
|
| 760 |
+
"affyio_check_cdf_type",
|
| 761 |
+
"affyio_read_cdffile_summary",
|
| 762 |
+
"affyio_get_package_version",
|
| 763 |
+
"alabaster_check",
|
| 764 |
+
"stage_sfe_object",
|
| 765 |
+
"load_sfe_object",
|
| 766 |
+
"save_spatial_experiment",
|
| 767 |
+
"read_spatial_experiment",
|
| 768 |
+
"rscript",
|
| 769 |
+
"annotationdbi_columns",
|
| 770 |
+
"annotationdbi_keytypes",
|
| 771 |
+
"annotationdbi_keys",
|
| 772 |
+
"annotationdbi_select",
|
| 773 |
+
"annotationdbi_mapids",
|
| 774 |
+
"create_individual_filter",
|
| 775 |
+
"parse_filter_formula",
|
| 776 |
+
"create_filter_list",
|
| 777 |
+
"get_filter_properties",
|
| 778 |
+
"list_supported_filters",
|
| 779 |
+
"translate_to_sql_where",
|
| 780 |
+
"run_r_script",
|
| 781 |
+
"run_apl_analysis",
|
| 782 |
+
"aw_weight",
|
| 783 |
+
"aw_mean",
|
| 784 |
+
"aw_median",
|
| 785 |
+
"banksy_init_object",
|
| 786 |
+
"banksy_run_banksy",
|
| 787 |
+
"banksy_cluster_banksy",
|
| 788 |
+
"banksy_spatial_dim_plot",
|
| 789 |
+
"rscript_run_script",
|
| 790 |
+
"rscript_run_expression",
|
| 791 |
+
"beachmat_inspect_matrix",
|
| 792 |
+
"rscript_get_version",
|
| 793 |
+
"run_benchdamic",
|
| 794 |
+
"generate_data",
|
| 795 |
+
"run_methods",
|
| 796 |
+
"evaluate_methods",
|
| 797 |
+
"plot_results",
|
| 798 |
+
"rscript_run",
|
| 799 |
+
"rscript_version",
|
| 800 |
+
"execute_r_script",
|
| 801 |
+
"biocfilecache_new",
|
| 802 |
+
"biocfilecache_add",
|
| 803 |
+
"biocfilecache_rpath",
|
| 804 |
+
"biocfilecache_query",
|
| 805 |
+
"biocfilecache_remove",
|
| 806 |
+
"biocfilecache_ls",
|
| 807 |
+
"biocfilecache_update",
|
| 808 |
+
"biocfilecache_clean",
|
| 809 |
+
"biocfilecache_info",
|
| 810 |
+
"rscript",
|
| 811 |
+
"biocio_import",
|
| 812 |
+
"biocio_export",
|
| 813 |
+
"run_rscript",
|
| 814 |
+
"bplapply",
|
| 815 |
+
"bpmapply",
|
| 816 |
+
"bpvec",
|
| 817 |
+
"bpaggregate",
|
| 818 |
+
"bpiterate",
|
| 819 |
+
"bpworkers",
|
| 820 |
+
"bpvalidate",
|
| 821 |
+
"biocsingular_run_svd",
|
| 822 |
+
"biocsingular_run_pca",
|
| 823 |
+
"biocsingular_get_info",
|
| 824 |
+
"run_rscript",
|
| 825 |
+
"get_rscript_version",
|
| 826 |
+
"read_biom_file",
|
| 827 |
+
"write_biom_file",
|
| 828 |
+
"rscript",
|
| 829 |
+
"biovizbase_get_ideogram",
|
| 830 |
+
"biovizbase_crunch",
|
| 831 |
+
"biovizbase_get_bio_color",
|
| 832 |
+
"biovizbase_calculate_islands",
|
| 833 |
+
"biovizbase_add_stepping",
|
| 834 |
+
"biovizbase_rescale_ranges",
|
| 835 |
+
"biovizbase_shrink_introns",
|
| 836 |
+
"blase_run",
|
| 837 |
+
"cluster_rows_kmeans",
|
| 838 |
+
"cluster_rows_hclust",
|
| 839 |
+
"cluster_rows_snn_graph",
|
| 840 |
+
"pairwise_rand_index",
|
| 841 |
+
"pairwise_jaccard_index",
|
| 842 |
+
"bulk_de",
|
| 843 |
+
"bulk_walk",
|
| 844 |
+
"signal_walk",
|
| 845 |
+
"cardspa",
|
| 846 |
+
"catscradle_build_neighborhoods",
|
| 847 |
+
"catscradle_gene_centric_analysis",
|
| 848 |
+
"catscradle_tag_neighborhoods",
|
| 849 |
+
"catscradle_spatial_vignette_pipeline",
|
| 850 |
+
"cdi_calculate",
|
| 851 |
+
"cdi_calculate_from_seurat",
|
| 852 |
+
"cdi_calculate_from_sce",
|
| 853 |
+
"cdi_plot",
|
| 854 |
+
"process_count_matrix",
|
| 855 |
+
"plot_normalization_qc",
|
| 856 |
+
"generate_cell_hashing_calls",
|
| 857 |
+
"summarize_cells_by_classification",
|
| 858 |
+
"get_example_markdown",
|
| 859 |
+
"call_and_generate_report",
|
| 860 |
+
"cellid_run_mca",
|
| 861 |
+
"cellid_get_cell_gene_set",
|
| 862 |
+
"cellid_run_cell_hgt",
|
| 863 |
+
"cellid_run_gsea",
|
| 864 |
+
"cellid_run_group_mca",
|
| 865 |
+
"run_cellmigration_analysis",
|
| 866 |
+
"cluster_fold_similarity",
|
| 867 |
+
"clustifyr_rscript",
|
| 868 |
+
"sig_clust",
|
| 869 |
+
"recluster",
|
| 870 |
+
"sim_sig",
|
| 871 |
+
"sim_null",
|
| 872 |
+
"make_complex_heatmap",
|
| 873 |
+
"compute_concordex",
|
| 874 |
+
"plot_concordex",
|
| 875 |
+
"run_cotan_analysis",
|
| 876 |
+
"csoa_analysis",
|
| 877 |
+
"run_ctsv",
|
| 878 |
+
"get_metadata",
|
| 879 |
+
"list_metadata_fields",
|
| 880 |
+
"search_metadata",
|
| 881 |
+
"query_metadata_custom",
|
| 882 |
+
"get_atlas_data",
|
| 883 |
+
"get_gene_expression",
|
| 884 |
+
"cytomapper_rscript",
|
| 885 |
+
"filter_and_trim",
|
| 886 |
+
"learn_errors",
|
| 887 |
+
"dada_denoise",
|
| 888 |
+
"merge_paired_reads",
|
| 889 |
+
"make_sequence_table",
|
| 890 |
+
"remove_bimera_denovo",
|
| 891 |
+
"assign_taxonomy",
|
| 892 |
+
"plot_quality_profile",
|
| 893 |
+
"plot_errors",
|
| 894 |
+
"install_bioconductor_data_package",
|
| 895 |
+
"list_bioconductor_data_packages",
|
| 896 |
+
"download_bioconductor_data_file",
|
| 897 |
+
"parse_bioconductor_yaml_metadata",
|
| 898 |
+
"search_bioconductor_data_packages",
|
| 899 |
+
"get_bioconductor_version_info",
|
| 900 |
+
"align_sequences",
|
| 901 |
+
"find_chimeras",
|
| 902 |
+
"classify_sequences",
|
| 903 |
+
"design_primers",
|
| 904 |
+
"design_probes",
|
| 905 |
+
"is_contaminant",
|
| 906 |
+
"decontx",
|
| 907 |
+
"decontpro",
|
| 908 |
+
"get_mean_ratio",
|
| 909 |
+
"find_markers_1v_all",
|
| 910 |
+
"plot_marker_expression",
|
| 911 |
+
"make_cell_colors",
|
| 912 |
+
"plot_set_basis",
|
| 913 |
+
"create_merged_sce",
|
| 914 |
+
"fastqc",
|
| 915 |
+
"cluster_scrnaseq",
|
| 916 |
+
"cluster_sp_data",
|
| 917 |
+
"run_despace",
|
| 918 |
+
"run_diffbind",
|
| 919 |
+
"normalize_single_cell_data",
|
| 920 |
+
"dirichlet_multinomial_dmn",
|
| 921 |
+
"dnacopy_segment",
|
| 922 |
+
"enrich_do",
|
| 923 |
+
"gse_do",
|
| 924 |
+
"enrich_ncg",
|
| 925 |
+
"gse_ncg",
|
| 926 |
+
"enrich_dgn",
|
| 927 |
+
"gse_dgn",
|
| 928 |
+
"create_ensdb_from_gtf",
|
| 929 |
+
"create_ensdb_from_gff",
|
| 930 |
+
"query_genes",
|
| 931 |
+
"query_transcripts",
|
| 932 |
+
"query_exons",
|
| 933 |
+
"query_promoters",
|
| 934 |
+
"run_erma_script",
|
| 935 |
+
"escher_convert",
|
| 936 |
+
"escher_clear_cache",
|
| 937 |
+
"escher_run",
|
| 938 |
+
"escher_launch",
|
| 939 |
+
"manage_experiment_subset",
|
| 940 |
+
"fgsea_run",
|
| 941 |
+
"fgsea_plot_enrichment",
|
| 942 |
+
"fgsea_plot_gsea_table",
|
| 943 |
+
"genefilter_nsfilter",
|
| 944 |
+
"genefilter_rowttests",
|
| 945 |
+
"genefilter_k_over_a",
|
| 946 |
+
"geneplotter_plot_ma",
|
| 947 |
+
"geneplotter_plot_densities",
|
| 948 |
+
"geneplotter_plot_pca",
|
| 949 |
+
"genomeinfodb_list_styles",
|
| 950 |
+
"genomeinfodb_map_seqlevels",
|
| 951 |
+
"genomeinfodb_get_seqinfo",
|
| 952 |
+
"genomeinfodb_rename_seqlevels",
|
| 953 |
+
"rscript_runner",
|
| 954 |
+
"rscript_version",
|
| 955 |
+
"summarize_overlaps",
|
| 956 |
+
"make_txdb_from_gff",
|
| 957 |
+
"granges_reduce",
|
| 958 |
+
"granges_intersect",
|
| 959 |
+
"granges_union",
|
| 960 |
+
"granges_setdiff",
|
| 961 |
+
"granges_find_overlaps",
|
| 962 |
+
"granges_flank",
|
| 963 |
+
"granges_resize",
|
| 964 |
+
"granges_shift",
|
| 965 |
+
"granges_coverage",
|
| 966 |
+
"granges_gaps",
|
| 967 |
+
"granges_narrow",
|
| 968 |
+
"read_nanostring_geomx_set",
|
| 969 |
+
"set_segment_qc_flags",
|
| 970 |
+
"set_bioprobe_qc_flags",
|
| 971 |
+
"subset_geomx_set",
|
| 972 |
+
"aggregate_counts",
|
| 973 |
+
"normalize_geomx",
|
| 974 |
+
"mixed_model_de",
|
| 975 |
+
"plot_reduced_dim",
|
| 976 |
+
"plot_gene_expression",
|
| 977 |
+
"plot_expression_heatmap",
|
| 978 |
+
"plot_expression_violin",
|
| 979 |
+
"ggspavis_plot_spots",
|
| 980 |
+
"ggspavis_plot_feature",
|
| 981 |
+
"ggspavis_plot_dim_red",
|
| 982 |
+
"ggspavis_plot_label",
|
| 983 |
+
"run_ggtree_script",
|
| 984 |
+
"fit_glm_gp",
|
| 985 |
+
"test_differential_expression",
|
| 986 |
+
"get_overdispersion_estimates",
|
| 987 |
+
"predict_glm_gp",
|
| 988 |
+
"list_go_db_columns",
|
| 989 |
+
"query_go_db",
|
| 990 |
+
"go_similarity",
|
| 991 |
+
"mgo_similarity",
|
| 992 |
+
"gene_similarity",
|
| 993 |
+
"mgene_similarity",
|
| 994 |
+
"cluster_similarity",
|
| 995 |
+
"mcluster_similarity",
|
| 996 |
+
"list_supported_orgdbs",
|
| 997 |
+
"rscript",
|
| 998 |
+
"gsva",
|
| 999 |
+
"hcatonsildata_load",
|
| 1000 |
+
"write_hdf5_array",
|
| 1001 |
+
"save_hdf5_summarized_experiment",
|
| 1002 |
+
"export_hdf5_summarized_experiment",
|
| 1003 |
+
"inspect_hdf5_array",
|
| 1004 |
+
"hoodscanr_estimate_radius",
|
| 1005 |
+
"hoodscanr_hoodscan",
|
| 1006 |
+
"hoodscanr_calc_colocalisation",
|
| 1007 |
+
"hoodscanr_calc_spatial_correlation",
|
| 1008 |
+
"hoodscanr_plot_colocalisation",
|
| 1009 |
+
"hoodscanr_plot_spatial_correlation",
|
| 1010 |
+
"list_humanhippocampus2024_datasets",
|
| 1011 |
+
"get_humanhippocampus2024_dataset",
|
| 1012 |
+
"download_imcdataset",
|
| 1013 |
+
"build_spatial_graph",
|
| 1014 |
+
"aggregate_neighbors",
|
| 1015 |
+
"test_interactions",
|
| 1016 |
+
"plot_spatial_graph",
|
| 1017 |
+
"impute_knn",
|
| 1018 |
+
"infercnv_run",
|
| 1019 |
+
"infercnv_plot",
|
| 1020 |
+
"infercnv_filter_genes",
|
| 1021 |
+
"interactive_display_base",
|
| 1022 |
+
"iranges_transform",
|
| 1023 |
+
"iranges_set_operations",
|
| 1024 |
+
"iranges_overlap_analysis",
|
| 1025 |
+
"iranges_nearest_methods",
|
| 1026 |
+
"iranges_coverage",
|
| 1027 |
+
"run_irisfgm_script",
|
| 1028 |
+
"create_spatial_vectors",
|
| 1029 |
+
"find_marker_genes_permutation",
|
| 1030 |
+
"find_marker_genes_linear_model",
|
| 1031 |
+
"kegg_info",
|
| 1032 |
+
"kegg_list",
|
| 1033 |
+
"kegg_find",
|
| 1034 |
+
"kegg_get",
|
| 1035 |
+
"kegg_conv",
|
| 1036 |
+
"kegg_link",
|
| 1037 |
+
"lisa_calculate",
|
| 1038 |
+
"lisa_cluster",
|
| 1039 |
+
"lisa_hatch_plot",
|
| 1040 |
+
"lisa_region_map",
|
| 1041 |
+
"lisa_heatmap",
|
| 1042 |
+
"mastr_align",
|
| 1043 |
+
"mastr_score_alignment",
|
| 1044 |
+
"mastr_check_dependencies",
|
| 1045 |
+
"perform_matrix_statistic",
|
| 1046 |
+
"list_merfish_datasets",
|
| 1047 |
+
"get_merfish_dataset",
|
| 1048 |
+
"rscript",
|
| 1049 |
+
"combine_p_values",
|
| 1050 |
+
"grouped_p_values",
|
| 1051 |
+
"run_mia_r_script",
|
| 1052 |
+
"read_xenium_to_molecule_experiment",
|
| 1053 |
+
"read_cosmx_to_molecule_experiment",
|
| 1054 |
+
"read_merscope_to_molecule_experiment",
|
| 1055 |
+
"count_molecules",
|
| 1056 |
+
"filter_molecules_by_gene",
|
| 1057 |
+
"plot_molecules_spatial",
|
| 1058 |
+
"create_molecule_experiment_from_df",
|
| 1059 |
+
"start_simulation",
|
| 1060 |
+
"mouse_gastrulation_data",
|
| 1061 |
+
"atlas_sample_metadata",
|
| 1062 |
+
"embryo_color_map",
|
| 1063 |
+
"mspurity_purity_a",
|
| 1064 |
+
"mspurity_purity_x",
|
| 1065 |
+
"mspurity_average_intensities",
|
| 1066 |
+
"mspurity_create_database",
|
| 1067 |
+
"mspurity_spectral_matching",
|
| 1068 |
+
"mspurity_filter_frag",
|
| 1069 |
+
"create_multiassayexperiment",
|
| 1070 |
+
"subset_by_assay",
|
| 1071 |
+
"subset_by_sample",
|
| 1072 |
+
"subset_by_row",
|
| 1073 |
+
"export_long_format",
|
| 1074 |
+
"multtest_mtp",
|
| 1075 |
+
"multtest_adjust_pvalues",
|
| 1076 |
+
"nebulosa_plot_density",
|
| 1077 |
+
"nnsvg",
|
| 1078 |
+
"noiseqbio",
|
| 1079 |
+
"noiseq",
|
| 1080 |
+
"predict_orf",
|
| 1081 |
+
"find_orfs",
|
| 1082 |
+
"classify_orfs",
|
| 1083 |
+
"vectorize_orfs",
|
| 1084 |
+
"annotate_orf",
|
| 1085 |
+
"select_annotations",
|
| 1086 |
+
"map_ids",
|
| 1087 |
+
"list_resources",
|
| 1088 |
+
"get_db_metadata",
|
| 1089 |
+
"get_available_keys",
|
| 1090 |
+
"get_species_info",
|
| 1091 |
+
"org_hs_eg_db_select",
|
| 1092 |
+
"org_hs_eg_db_keytypes",
|
| 1093 |
+
"org_hs_eg_db_columns",
|
| 1094 |
+
"org_hs_eg_db_map_symbol_to_entrez",
|
| 1095 |
+
"org_hs_eg_db_get_keys",
|
| 1096 |
+
"org_hs_eg_db_metadata",
|
| 1097 |
+
"org_hs_eg_db_map_ids",
|
| 1098 |
+
"org_mm_eg_db_query",
|
| 1099 |
+
"org_mm_eg_db_list_columns",
|
| 1100 |
+
"org_mm_eg_db_list_keytypes",
|
| 1101 |
+
"org_mm_eg_db_list_keys",
|
| 1102 |
+
"partcnv_classify",
|
| 1103 |
+
"partcnvh_classify",
|
| 1104 |
+
"get_partcnv_gene_info",
|
| 1105 |
+
"rscript",
|
| 1106 |
+
"phyloseq_filter_and_transform",
|
| 1107 |
+
"phyloseq_plot_ordination",
|
| 1108 |
+
"phyloseq_plot_richness",
|
| 1109 |
+
"phyloseq_plot_heatmap",
|
| 1110 |
+
"pipecomp_run",
|
| 1111 |
+
"poem_evaluate",
|
| 1112 |
+
"preprocesscore_normalize_quantiles",
|
| 1113 |
+
"preprocesscore_normalize_quantiles_robust",
|
| 1114 |
+
"preprocesscore_background_correct",
|
| 1115 |
+
"preprocesscore_sub_col_summarize_median_polish",
|
| 1116 |
+
"preprocesscore_sub_col_summarize_log_avg",
|
| 1117 |
+
"preprocesscore_sub_col_summarize_log_median",
|
| 1118 |
+
"preprocesscore_sub_col_summarize_biweight_midavg",
|
| 1119 |
+
"proteomicsannotationhubdata_rscript",
|
| 1120 |
+
"run_r_script",
|
| 1121 |
+
"run_qvalue",
|
| 1122 |
+
"execute_rbgl_r_code",
|
| 1123 |
+
"get_citation",
|
| 1124 |
+
"regional_limma",
|
| 1125 |
+
"regional_voom",
|
| 1126 |
+
"regional_wilcox",
|
| 1127 |
+
"regional_ttest",
|
| 1128 |
+
"rscript",
|
| 1129 |
+
"plot_graph",
|
| 1130 |
+
"run_rhdf5_r_script",
|
| 1131 |
+
"check_installation",
|
| 1132 |
+
"rhdf5lib_info",
|
| 1133 |
+
"rscript_run",
|
| 1134 |
+
"rsamtools_index_bam",
|
| 1135 |
+
"rsamtools_sort_bam",
|
| 1136 |
+
"rsamtools_merge_bam",
|
| 1137 |
+
"rsamtools_idxstats_bam",
|
| 1138 |
+
"rsamtools_pileup",
|
| 1139 |
+
"rsubread_buildindex",
|
| 1140 |
+
"rsubread_align",
|
| 1141 |
+
"rsubread_subjunc",
|
| 1142 |
+
"rsubread_featurecounts",
|
| 1143 |
+
"rsubread_qualityscores",
|
| 1144 |
+
"rsubread_atgccontent",
|
| 1145 |
+
"rsubread_propmapped",
|
| 1146 |
+
"create_scaled_matrix",
|
| 1147 |
+
"realize_scaled_matrix",
|
| 1148 |
+
"get_centering_vector",
|
| 1149 |
+
"get_scaling_factor",
|
| 1150 |
+
"get_unscaled_matrix",
|
| 1151 |
+
"get_scaled_matrix_metadata",
|
| 1152 |
+
"scalign",
|
| 1153 |
+
"create_gds_seurat_object",
|
| 1154 |
+
"run_scbfa",
|
| 1155 |
+
"scbubbletree",
|
| 1156 |
+
"run_rscript",
|
| 1157 |
+
"scclassifr_train",
|
| 1158 |
+
"scclassifr_predict",
|
| 1159 |
+
"scclassifr_classify",
|
| 1160 |
+
"rscript",
|
| 1161 |
+
"rscript_version",
|
| 1162 |
+
"sc_dot_plot",
|
| 1163 |
+
"sc_dot_plot_data",
|
| 1164 |
+
"sc_dot_plot_custom_df",
|
| 1165 |
+
"scfeatures",
|
| 1166 |
+
"recluster",
|
| 1167 |
+
"find_isc",
|
| 1168 |
+
"find_de_genes",
|
| 1169 |
+
"find_dr_genes",
|
| 1170 |
+
"run_scider",
|
| 1171 |
+
"scmageck_eff_estimate",
|
| 1172 |
+
"scmageck_lr",
|
| 1173 |
+
"scmageck_optim_perturb",
|
| 1174 |
+
"scmageck_get_score",
|
| 1175 |
+
"run_scqtl_pipeline",
|
| 1176 |
+
"scran_normalize",
|
| 1177 |
+
"rscript",
|
| 1178 |
+
"run_rscript",
|
| 1179 |
+
"generate_cluster_tree",
|
| 1180 |
+
"normalize_counts",
|
| 1181 |
+
"aggregate_across_cells",
|
| 1182 |
+
"scvir_get_pbmc_cite_data",
|
| 1183 |
+
"scvir_get_totalvi_tutorial_data",
|
| 1184 |
+
"scvir_run_totalvi_pipeline",
|
| 1185 |
+
"scvir_run_demo",
|
| 1186 |
+
"scvir_extract_latent",
|
| 1187 |
+
"rasterize_gene",
|
| 1188 |
+
"rasterize_cell_type",
|
| 1189 |
+
"seraster_wrapper",
|
| 1190 |
+
"shortread_qa",
|
| 1191 |
+
"shortread_trim_tails",
|
| 1192 |
+
"shortread_filter_n",
|
| 1193 |
+
"shortread_alphabet_frequency",
|
| 1194 |
+
"shortread_fastq_count",
|
| 1195 |
+
"shortread_trim_lr_patterns",
|
| 1196 |
+
"signifinder",
|
| 1197 |
+
"rscript",
|
| 1198 |
+
"run_smoothclust_analysis",
|
| 1199 |
+
"aggregate",
|
| 1200 |
+
"coloc",
|
| 1201 |
+
"gradient",
|
| 1202 |
+
"vicinity",
|
| 1203 |
+
"find_structure",
|
| 1204 |
+
"get_structure_metrics",
|
| 1205 |
+
"find_structure_neighbors",
|
| 1206 |
+
"get_structure_aggregated_expression",
|
| 1207 |
+
"spacetrooper_deconvolve",
|
| 1208 |
+
"spacetrooper_extract_weights",
|
| 1209 |
+
"spacetrooper_plot_spatial_weights",
|
| 1210 |
+
"spacetrooper_compute_interactions",
|
| 1211 |
+
"spacetrooper_check_convergence",
|
| 1212 |
+
"rscript",
|
| 1213 |
+
"preprocess_spatial_data",
|
| 1214 |
+
"analyze_spatial_data",
|
| 1215 |
+
"plot_spatial_results",
|
| 1216 |
+
"run_sparse_matrix_stats",
|
| 1217 |
+
"run_rscript",
|
| 1218 |
+
"list_datasets",
|
| 1219 |
+
"get_dataset_info",
|
| 1220 |
+
"download_dataset",
|
| 1221 |
+
"spatialdecon_rscript",
|
| 1222 |
+
"fetch_spatial_dmelxsim_rds",
|
| 1223 |
+
"export_spatial_dmelxsim_to_csv",
|
| 1224 |
+
"get_spatial_dmelxsim_summary",
|
| 1225 |
+
"run_custom_spatial_dmelxsim_query",
|
| 1226 |
+
"rscript",
|
| 1227 |
+
"read_xenium",
|
| 1228 |
+
"read_cosmx",
|
| 1229 |
+
"read_merscope",
|
| 1230 |
+
"read_starmap_plus",
|
| 1231 |
+
"spatial_fda_fit",
|
| 1232 |
+
"spatial_fda_predict",
|
| 1233 |
+
"spatial_fda_fpca",
|
| 1234 |
+
"spatial_fda_summary_stats",
|
| 1235 |
+
"spatial_fda_plot",
|
| 1236 |
+
"run_spatialfeatureexperiment_script",
|
| 1237 |
+
"spatial_heatmap",
|
| 1238 |
+
"spatial_enrichment",
|
| 1239 |
+
"spatial_network",
|
| 1240 |
+
"spatial_cluster",
|
| 1241 |
+
"validate_svg_mapping",
|
| 1242 |
+
"propeller",
|
| 1243 |
+
"get_transformed_props",
|
| 1244 |
+
"normalize_to_median",
|
| 1245 |
+
"plot_props",
|
| 1246 |
+
"plot_cell_counts",
|
| 1247 |
+
"run_spoon",
|
| 1248 |
+
"spotclean",
|
| 1249 |
+
"local_outliers",
|
| 1250 |
+
"find_artifacts",
|
| 1251 |
+
"plot_qc",
|
| 1252 |
+
"dist_to_nearest",
|
| 1253 |
+
"run_standr_analysis",
|
| 1254 |
+
"statial_calc_interactions",
|
| 1255 |
+
"statial_get_spatial_context",
|
| 1256 |
+
"statial_bivariate_test",
|
| 1257 |
+
"statial_impute_interactions",
|
| 1258 |
+
"statial_get_interactions",
|
| 1259 |
+
"stjoincount_find_colocalized_genes",
|
| 1260 |
+
"stjoincount_moran_mc",
|
| 1261 |
+
"stjoincount_joincount_mc",
|
| 1262 |
+
"stjoincount_joincount_lisa",
|
| 1263 |
+
"execute_r_script_with_summarizedexperiment",
|
| 1264 |
+
"svp_train",
|
| 1265 |
+
"svp_predict",
|
| 1266 |
+
"load_tenx_xenium_data",
|
| 1267 |
+
"tidyomics_list_packages",
|
| 1268 |
+
"tidyomics_attach_packages",
|
| 1269 |
+
"tidyomics_check_conflicts",
|
| 1270 |
+
"run_tidyspatialexperiment_script",
|
| 1271 |
+
"create_tree_summarized_experiment",
|
| 1272 |
+
"tximport",
|
| 1273 |
+
"summarize_to_gene",
|
| 1274 |
+
"make_tx2gene_from_gtf",
|
| 1275 |
+
"predict_coding",
|
| 1276 |
+
"locate_variants",
|
| 1277 |
+
"filter_vcf",
|
| 1278 |
+
"get_human_lung_cancer_vectra",
|
| 1279 |
+
"get_human_ovarian_cancer_vectra_polaris",
|
| 1280 |
+
"list_vectra_polaris_datasets",
|
| 1281 |
+
"inspect_vectra_rds",
|
| 1282 |
+
"read_visium",
|
| 1283 |
+
"write_visium",
|
| 1284 |
+
"load_weberdivechalc_data",
|
| 1285 |
+
"run_xcms_r_script",
|
| 1286 |
+
"xenlite_import_xenium",
|
| 1287 |
+
"xenlite_to_spatial_experiment",
|
| 1288 |
+
"xenlite_extract_transcripts",
|
| 1289 |
+
"xenlite_get_summary",
|
| 1290 |
+
"xenlite_plot_spatial",
|
| 1291 |
+
"xvector_get_info",
|
| 1292 |
+
"xvector_subseq",
|
| 1293 |
+
"xvector_narrow",
|
| 1294 |
+
"xvector_compact",
|
| 1295 |
+
"xvector_slice",
|
| 1296 |
+
"xvector_to_raw",
|
| 1297 |
+
"xvector_aggregate",
|
| 1298 |
+
"xvector_create_from_list",
|
| 1299 |
+
"run_rscript",
|
| 1300 |
+
"run_script",
|
| 1301 |
+
"perl",
|
| 1302 |
+
"run_perl_script",
|
| 1303 |
+
"bpipe_run",
|
| 1304 |
+
"bpipe_test",
|
| 1305 |
+
"bpipe_retry",
|
| 1306 |
+
"bpipe_list",
|
| 1307 |
+
"bpipe_log",
|
| 1308 |
+
"bpipe_history",
|
| 1309 |
+
"bpipe_status",
|
| 1310 |
+
"bpipe_clean",
|
| 1311 |
+
"bpipe_version",
|
| 1312 |
+
"run_brooklyn_plot",
|
| 1313 |
+
"busco_run",
|
| 1314 |
+
"busco_list_datasets",
|
| 1315 |
+
"busco_download",
|
| 1316 |
+
"busco_plot",
|
| 1317 |
+
"bed_intersect",
|
| 1318 |
+
"maf_filter",
|
| 1319 |
+
"fasta_formatter",
|
| 1320 |
+
"wig_to_bigwig",
|
| 1321 |
+
"get_flanking_sequences",
|
| 1322 |
+
"adig",
|
| 1323 |
+
"ahost",
|
| 1324 |
+
"discover",
|
| 1325 |
+
"acyclify",
|
| 1326 |
+
"tune",
|
| 1327 |
+
"deduce",
|
| 1328 |
+
"design",
|
| 1329 |
+
"upgrade",
|
| 1330 |
+
"device_manager",
|
| 1331 |
+
"cd_hit",
|
| 1332 |
+
"cdbfasta",
|
| 1333 |
+
"cdbyank",
|
| 1334 |
+
"cdbyank_list",
|
| 1335 |
+
"interaction_pipeline",
|
| 1336 |
+
"tensor_pipeline",
|
| 1337 |
+
"run_cellitac_pipeline",
|
| 1338 |
+
"run_cellqc",
|
| 1339 |
+
"cellrank_run_analysis",
|
| 1340 |
+
"cellsnake_install",
|
| 1341 |
+
"celltypist_predict",
|
| 1342 |
+
"celltypist_show_models",
|
| 1343 |
+
"celltypist_update_models",
|
| 1344 |
+
"predict",
|
| 1345 |
+
"train",
|
| 1346 |
+
"checkatlas",
|
| 1347 |
+
"data",
|
| 1348 |
+
"lineage_wf",
|
| 1349 |
+
"taxonomy_wf",
|
| 1350 |
+
"tree_wf",
|
| 1351 |
+
"tree",
|
| 1352 |
+
"qa",
|
| 1353 |
+
"plot",
|
| 1354 |
+
"ssu_finder",
|
| 1355 |
+
"unique_markers",
|
| 1356 |
+
"profile",
|
| 1357 |
+
"tetra",
|
| 1358 |
+
"dist",
|
| 1359 |
+
"coverage",
|
| 1360 |
+
"len_hist",
|
| 1361 |
+
"nx_plot",
|
| 1362 |
+
"bin_set"
|
| 1363 |
+
]
|
| 1364 |
+
}
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/run_metadata.json
ADDED
|
@@ -0,0 +1,32 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"task_id": "alzheimer-mouse",
|
| 3 |
+
"task_name": "Alzheimer Mouse Models: Comparative Pathway Analysis",
|
| 4 |
+
"run_dir": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826",
|
| 5 |
+
"dataset_dir": "/225040511/project/bioagent-bench/dataset/alzheimer-mouse",
|
| 6 |
+
"data_dir": "/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data",
|
| 7 |
+
"reference_dir": "/225040511/project/bioagent-bench/dataset/alzheimer-mouse/reference",
|
| 8 |
+
"agent_runtime_dir": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/agent_runtime",
|
| 9 |
+
"output_paths": [
|
| 10 |
+
"/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/pathway_comparison.csv"
|
| 11 |
+
],
|
| 12 |
+
"mcp_config": "/225040511/project/Biomni/experiments/bioagent_bench/configs/mcp_scale_1000.yaml",
|
| 13 |
+
"agent_kwargs": {
|
| 14 |
+
"path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/agent_runtime",
|
| 15 |
+
"expected_data_lake_files": [],
|
| 16 |
+
"use_tool_retriever": true,
|
| 17 |
+
"timeout_seconds": 1200,
|
| 18 |
+
"llm": "deepseek-v4-flash",
|
| 19 |
+
"source": "Custom",
|
| 20 |
+
"base_url": "https://api.deepseek.com/v1",
|
| 21 |
+
"api_key": "sk-06e6154722b84e89b081b1c9571838ef"
|
| 22 |
+
},
|
| 23 |
+
"query": "You are running a bioagent-bench task with local files already prepared.\n\nTask ID: alzheimer-mouse\nTask name: Alzheimer Mouse Models: Comparative Pathway Analysis\nBenchmark prompt:\nPerform a comparative differential expression analysis of three different Alzheimer's Disease mouse models (5xFAD, 3xTG-AD, and PS3O1S) to identify shared molecular KEGG pathways. The output should be a CSV file with the following columns: 'pathway','5xFAD_pvalue','3xTG_AD_pvalue','PS3O1S_pvalue'. Example csv <example>Pathway,5xFAD_pvalue,3xTG_AD_pvalue,PS3O1S_pvalue\nPhagosome Homo sapiens hsa04145,1.5045916403148935e-09,0.3102788532065793,0.4443015705596512\n</example> \nData background:\nAnalyze 5xFAD, 3xTG-AD, and PS301S mouse models: normalize counts, perform differential expression, run KEGG pathway enrichment, and compare shared pathways across models.\n\nConstraints:\n1. Use only the benchmark inputs and references explicitly listed below.\n2. Save the required final deliverables exactly to the paths listed below.\n3. Save all intermediate scripts, logs, and scratch outputs inside this run directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826\n4. Keep final deliverables in the same schema/format requested by the benchmark prompt.\n5. Return a concise final summary after writing the required files.\n\nTask-specific instruction:\nUse the provided mouse count and DEA files as inputs. Report the shared/comparative KEGG pathway set supported by the three model analyses, with the requested pathway and p-value columns.\n\nBenchmark data policy:\n- Allowed input data directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data\n- Allowed reference directory: <none>\n- Allowed scratch/output directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826\n- Forbidden truth/results directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/results\n- Forbidden sibling benchmark task directories: /225040511/project/bioagent-bench/dataset/<any task other than alzheimer-mouse>\n- Do not inspect previous bioagent-bench-runs or sibling task outputs as data sources.\n- Do not download external databases or install new packages during the benchmark run.\n\nInput data directory:\n/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data\nVisible input files:\n- DEA_PS3O1S.csv\n- GSE161904_Raw_gene_counts_cortex.txt\n- GSE168137_countList.txt\n\nReference data directory:\n<none>\nVisible reference files:\n- <none>\n\nRequired final output paths:\n- pathway_comparison.csv: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/pathway_comparison.csv",
|
| 24 |
+
"timestamp_utc": "20260515_133826",
|
| 25 |
+
"runtime_environment": {
|
| 26 |
+
"execution_env_prefix": "/225040511/miniconda3/envs/biomni_e1",
|
| 27 |
+
"execution_python": "/225040511/miniconda3/envs/biomni_e1/bin/python",
|
| 28 |
+
"conda_default_env": "biomni_e1",
|
| 29 |
+
"conda_prefix": "/225040511/miniconda3/envs/biomni_e1"
|
| 30 |
+
},
|
| 31 |
+
"biomni_root": "/225040511/project/Biomni"
|
| 32 |
+
}
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/sig_genes_5xfad.txt
ADDED
|
@@ -0,0 +1,2468 @@
|
|
|
|
|
|
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|
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|
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|
|
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|
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|
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|
| 2201 |
+
ENSMUSG00000085208
|
| 2202 |
+
ENSMUSG00000085251
|
| 2203 |
+
ENSMUSG00000085385
|
| 2204 |
+
ENSMUSG00000085389
|
| 2205 |
+
ENSMUSG00000085398
|
| 2206 |
+
ENSMUSG00000085438
|
| 2207 |
+
ENSMUSG00000085472
|
| 2208 |
+
ENSMUSG00000085564
|
| 2209 |
+
ENSMUSG00000085565
|
| 2210 |
+
ENSMUSG00000085912
|
| 2211 |
+
ENSMUSG00000085939
|
| 2212 |
+
ENSMUSG00000085957
|
| 2213 |
+
ENSMUSG00000085967
|
| 2214 |
+
ENSMUSG00000086058
|
| 2215 |
+
ENSMUSG00000086098
|
| 2216 |
+
ENSMUSG00000086109
|
| 2217 |
+
ENSMUSG00000086111
|
| 2218 |
+
ENSMUSG00000086287
|
| 2219 |
+
ENSMUSG00000086491
|
| 2220 |
+
ENSMUSG00000086564
|
| 2221 |
+
ENSMUSG00000086652
|
| 2222 |
+
ENSMUSG00000086693
|
| 2223 |
+
ENSMUSG00000086763
|
| 2224 |
+
ENSMUSG00000086804
|
| 2225 |
+
ENSMUSG00000086844
|
| 2226 |
+
ENSMUSG00000086905
|
| 2227 |
+
ENSMUSG00000086995
|
| 2228 |
+
ENSMUSG00000087014
|
| 2229 |
+
ENSMUSG00000087022
|
| 2230 |
+
ENSMUSG00000087052
|
| 2231 |
+
ENSMUSG00000087055
|
| 2232 |
+
ENSMUSG00000087107
|
| 2233 |
+
ENSMUSG00000087400
|
| 2234 |
+
ENSMUSG00000087524
|
| 2235 |
+
ENSMUSG00000087543
|
| 2236 |
+
ENSMUSG00000087593
|
| 2237 |
+
ENSMUSG00000089661
|
| 2238 |
+
ENSMUSG00000089695
|
| 2239 |
+
ENSMUSG00000089797
|
| 2240 |
+
ENSMUSG00000089832
|
| 2241 |
+
ENSMUSG00000089837
|
| 2242 |
+
ENSMUSG00000089929
|
| 2243 |
+
ENSMUSG00000089975
|
| 2244 |
+
ENSMUSG00000090035
|
| 2245 |
+
ENSMUSG00000090066
|
| 2246 |
+
ENSMUSG00000090098
|
| 2247 |
+
ENSMUSG00000090122
|
| 2248 |
+
ENSMUSG00000090124
|
| 2249 |
+
ENSMUSG00000090164
|
| 2250 |
+
ENSMUSG00000090439
|
| 2251 |
+
ENSMUSG00000090467
|
| 2252 |
+
ENSMUSG00000090486
|
| 2253 |
+
ENSMUSG00000090625
|
| 2254 |
+
ENSMUSG00000090675
|
| 2255 |
+
ENSMUSG00000090894
|
| 2256 |
+
ENSMUSG00000090942
|
| 2257 |
+
ENSMUSG00000091275
|
| 2258 |
+
ENSMUSG00000091337
|
| 2259 |
+
ENSMUSG00000091387
|
| 2260 |
+
ENSMUSG00000091549
|
| 2261 |
+
ENSMUSG00000091568
|
| 2262 |
+
ENSMUSG00000091649
|
| 2263 |
+
ENSMUSG00000092009
|
| 2264 |
+
ENSMUSG00000092021
|
| 2265 |
+
ENSMUSG00000092056
|
| 2266 |
+
ENSMUSG00000092242
|
| 2267 |
+
ENSMUSG00000092274
|
| 2268 |
+
ENSMUSG00000093456
|
| 2269 |
+
ENSMUSG00000093938
|
| 2270 |
+
ENSMUSG00000094113
|
| 2271 |
+
ENSMUSG00000094483
|
| 2272 |
+
ENSMUSG00000094708
|
| 2273 |
+
ENSMUSG00000094724
|
| 2274 |
+
ENSMUSG00000094796
|
| 2275 |
+
ENSMUSG00000094852
|
| 2276 |
+
ENSMUSG00000095079
|
| 2277 |
+
ENSMUSG00000095139
|
| 2278 |
+
ENSMUSG00000095276
|
| 2279 |
+
ENSMUSG00000095295
|
| 2280 |
+
ENSMUSG00000095577
|
| 2281 |
+
ENSMUSG00000095595
|
| 2282 |
+
ENSMUSG00000095687
|
| 2283 |
+
ENSMUSG00000095789
|
| 2284 |
+
ENSMUSG00000096014
|
| 2285 |
+
ENSMUSG00000096145
|
| 2286 |
+
ENSMUSG00000096351
|
| 2287 |
+
ENSMUSG00000096488
|
| 2288 |
+
ENSMUSG00000096617
|
| 2289 |
+
ENSMUSG00000096699
|
| 2290 |
+
ENSMUSG00000096727
|
| 2291 |
+
ENSMUSG00000096883
|
| 2292 |
+
ENSMUSG00000096914
|
| 2293 |
+
ENSMUSG00000096988
|
| 2294 |
+
ENSMUSG00000097002
|
| 2295 |
+
ENSMUSG00000097079
|
| 2296 |
+
ENSMUSG00000097129
|
| 2297 |
+
ENSMUSG00000097154
|
| 2298 |
+
ENSMUSG00000097194
|
| 2299 |
+
ENSMUSG00000097217
|
| 2300 |
+
ENSMUSG00000097237
|
| 2301 |
+
ENSMUSG00000097245
|
| 2302 |
+
ENSMUSG00000097281
|
| 2303 |
+
ENSMUSG00000097318
|
| 2304 |
+
ENSMUSG00000097339
|
| 2305 |
+
ENSMUSG00000097352
|
| 2306 |
+
ENSMUSG00000097365
|
| 2307 |
+
ENSMUSG00000097397
|
| 2308 |
+
ENSMUSG00000097404
|
| 2309 |
+
ENSMUSG00000097415
|
| 2310 |
+
ENSMUSG00000097471
|
| 2311 |
+
ENSMUSG00000097505
|
| 2312 |
+
ENSMUSG00000097558
|
| 2313 |
+
ENSMUSG00000097585
|
| 2314 |
+
ENSMUSG00000097654
|
| 2315 |
+
ENSMUSG00000097715
|
| 2316 |
+
ENSMUSG00000097788
|
| 2317 |
+
ENSMUSG00000097814
|
| 2318 |
+
ENSMUSG00000097885
|
| 2319 |
+
ENSMUSG00000098065
|
| 2320 |
+
ENSMUSG00000098112
|
| 2321 |
+
ENSMUSG00000098188
|
| 2322 |
+
ENSMUSG00000098395
|
| 2323 |
+
ENSMUSG00000098758
|
| 2324 |
+
ENSMUSG00000098781
|
| 2325 |
+
ENSMUSG00000098789
|
| 2326 |
+
ENSMUSG00000098973
|
| 2327 |
+
ENSMUSG00000099170
|
| 2328 |
+
ENSMUSG00000099404
|
| 2329 |
+
ENSMUSG00000099564
|
| 2330 |
+
ENSMUSG00000099839
|
| 2331 |
+
ENSMUSG00000099974
|
| 2332 |
+
ENSMUSG00000100029
|
| 2333 |
+
ENSMUSG00000100147
|
| 2334 |
+
ENSMUSG00000100396
|
| 2335 |
+
ENSMUSG00000100789
|
| 2336 |
+
ENSMUSG00000100794
|
| 2337 |
+
ENSMUSG00000100916
|
| 2338 |
+
ENSMUSG00000100980
|
| 2339 |
+
ENSMUSG00000101013
|
| 2340 |
+
ENSMUSG00000101585
|
| 2341 |
+
ENSMUSG00000101903
|
| 2342 |
+
ENSMUSG00000101995
|
| 2343 |
+
ENSMUSG00000102037
|
| 2344 |
+
ENSMUSG00000102353
|
| 2345 |
+
ENSMUSG00000102493
|
| 2346 |
+
ENSMUSG00000102719
|
| 2347 |
+
ENSMUSG00000102937
|
| 2348 |
+
ENSMUSG00000102964
|
| 2349 |
+
ENSMUSG00000102994
|
| 2350 |
+
ENSMUSG00000103320
|
| 2351 |
+
ENSMUSG00000103367
|
| 2352 |
+
ENSMUSG00000103731
|
| 2353 |
+
ENSMUSG00000103984
|
| 2354 |
+
ENSMUSG00000104000
|
| 2355 |
+
ENSMUSG00000104117
|
| 2356 |
+
ENSMUSG00000104204
|
| 2357 |
+
ENSMUSG00000104213
|
| 2358 |
+
ENSMUSG00000104299
|
| 2359 |
+
ENSMUSG00000104318
|
| 2360 |
+
ENSMUSG00000104484
|
| 2361 |
+
ENSMUSG00000104496
|
| 2362 |
+
ENSMUSG00000104507
|
| 2363 |
+
ENSMUSG00000104515
|
| 2364 |
+
ENSMUSG00000104535
|
| 2365 |
+
ENSMUSG00000104639
|
| 2366 |
+
ENSMUSG00000104713
|
| 2367 |
+
ENSMUSG00000104835
|
| 2368 |
+
ENSMUSG00000104918
|
| 2369 |
+
ENSMUSG00000105065
|
| 2370 |
+
ENSMUSG00000105076
|
| 2371 |
+
ENSMUSG00000105096
|
| 2372 |
+
ENSMUSG00000105398
|
| 2373 |
+
ENSMUSG00000105504
|
| 2374 |
+
ENSMUSG00000105769
|
| 2375 |
+
ENSMUSG00000105784
|
| 2376 |
+
ENSMUSG00000105945
|
| 2377 |
+
ENSMUSG00000105987
|
| 2378 |
+
ENSMUSG00000106219
|
| 2379 |
+
ENSMUSG00000106304
|
| 2380 |
+
ENSMUSG00000106433
|
| 2381 |
+
ENSMUSG00000106491
|
| 2382 |
+
ENSMUSG00000106492
|
| 2383 |
+
ENSMUSG00000106631
|
| 2384 |
+
ENSMUSG00000106734
|
| 2385 |
+
ENSMUSG00000106775
|
| 2386 |
+
ENSMUSG00000106917
|
| 2387 |
+
ENSMUSG00000107272
|
| 2388 |
+
ENSMUSG00000107314
|
| 2389 |
+
ENSMUSG00000107667
|
| 2390 |
+
ENSMUSG00000107736
|
| 2391 |
+
ENSMUSG00000107881
|
| 2392 |
+
ENSMUSG00000107978
|
| 2393 |
+
ENSMUSG00000108120
|
| 2394 |
+
ENSMUSG00000108325
|
| 2395 |
+
ENSMUSG00000108353
|
| 2396 |
+
ENSMUSG00000108388
|
| 2397 |
+
ENSMUSG00000108578
|
| 2398 |
+
ENSMUSG00000108601
|
| 2399 |
+
ENSMUSG00000108841
|
| 2400 |
+
ENSMUSG00000109556
|
| 2401 |
+
ENSMUSG00000109598
|
| 2402 |
+
ENSMUSG00000109644
|
| 2403 |
+
ENSMUSG00000109713
|
| 2404 |
+
ENSMUSG00000109854
|
| 2405 |
+
ENSMUSG00000109927
|
| 2406 |
+
ENSMUSG00000110165
|
| 2407 |
+
ENSMUSG00000110167
|
| 2408 |
+
ENSMUSG00000110235
|
| 2409 |
+
ENSMUSG00000110332
|
| 2410 |
+
ENSMUSG00000110611
|
| 2411 |
+
ENSMUSG00000110702
|
| 2412 |
+
ENSMUSG00000111147
|
| 2413 |
+
ENSMUSG00000111172
|
| 2414 |
+
ENSMUSG00000111219
|
| 2415 |
+
ENSMUSG00000111535
|
| 2416 |
+
ENSMUSG00000111895
|
| 2417 |
+
ENSMUSG00000111971
|
| 2418 |
+
ENSMUSG00000111977
|
| 2419 |
+
ENSMUSG00000112023
|
| 2420 |
+
ENSMUSG00000112148
|
| 2421 |
+
ENSMUSG00000112449
|
| 2422 |
+
ENSMUSG00000112548
|
| 2423 |
+
ENSMUSG00000113088
|
| 2424 |
+
ENSMUSG00000113102
|
| 2425 |
+
ENSMUSG00000113137
|
| 2426 |
+
ENSMUSG00000113621
|
| 2427 |
+
ENSMUSG00000113856
|
| 2428 |
+
ENSMUSG00000114432
|
| 2429 |
+
ENSMUSG00000114733
|
| 2430 |
+
ENSMUSG00000115008
|
| 2431 |
+
ENSMUSG00000115219
|
| 2432 |
+
ENSMUSG00000115230
|
| 2433 |
+
ENSMUSG00000115338
|
| 2434 |
+
ENSMUSG00000115391
|
| 2435 |
+
ENSMUSG00000115497
|
| 2436 |
+
ENSMUSG00000115529
|
| 2437 |
+
ENSMUSG00000115662
|
| 2438 |
+
ENSMUSG00000115813
|
| 2439 |
+
ENSMUSG00000115902
|
| 2440 |
+
ENSMUSG00000115928
|
| 2441 |
+
ENSMUSG00000115969
|
| 2442 |
+
ENSMUSG00000116097
|
| 2443 |
+
ENSMUSG00000116114
|
| 2444 |
+
ENSMUSG00000116180
|
| 2445 |
+
ENSMUSG00000116594
|
| 2446 |
+
ENSMUSG00000116607
|
| 2447 |
+
ENSMUSG00000116780
|
| 2448 |
+
ENSMUSG00000116884
|
| 2449 |
+
ENSMUSG00000116995
|
| 2450 |
+
ENSMUSG00000117003
|
| 2451 |
+
ENSMUSG00000117011
|
| 2452 |
+
ENSMUSG00000117254
|
| 2453 |
+
ENSMUSG00000117315
|
| 2454 |
+
ENSMUSG00000117333
|
| 2455 |
+
ENSMUSG00000117416
|
| 2456 |
+
ENSMUSG00000117421
|
| 2457 |
+
ENSMUSG00000117520
|
| 2458 |
+
ENSMUSG00000117521
|
| 2459 |
+
ENSMUSG00000117541
|
| 2460 |
+
ENSMUSG00000117592
|
| 2461 |
+
ENSMUSG00000117613
|
| 2462 |
+
ENSMUSG00000117763
|
| 2463 |
+
ENSMUSG00000117864
|
| 2464 |
+
ENSMUSG00000117926
|
| 2465 |
+
ENSMUSG00000117957
|
| 2466 |
+
ENSMUSG00000118125
|
| 2467 |
+
ENSMUSG00000118198
|
| 2468 |
+
ENSMUSG00000118346
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826/sig_genes_ps3o1s.txt
ADDED
|
@@ -0,0 +1,797 @@
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| 574 |
+
ENSMUSG00000075707
|
| 575 |
+
ENSMUSG00000076928
|
| 576 |
+
ENSMUSG00000078190
|
| 577 |
+
ENSMUSG00000078247
|
| 578 |
+
ENSMUSG00000078365
|
| 579 |
+
ENSMUSG00000078441
|
| 580 |
+
ENSMUSG00000078484
|
| 581 |
+
ENSMUSG00000078584
|
| 582 |
+
ENSMUSG00000078695
|
| 583 |
+
ENSMUSG00000078919
|
| 584 |
+
ENSMUSG00000079450
|
| 585 |
+
ENSMUSG00000079610
|
| 586 |
+
ENSMUSG00000079657
|
| 587 |
+
ENSMUSG00000079737
|
| 588 |
+
ENSMUSG00000079834
|
| 589 |
+
ENSMUSG00000080824
|
| 590 |
+
ENSMUSG00000080839
|
| 591 |
+
ENSMUSG00000080994
|
| 592 |
+
ENSMUSG00000081003
|
| 593 |
+
ENSMUSG00000081058
|
| 594 |
+
ENSMUSG00000081123
|
| 595 |
+
ENSMUSG00000081265
|
| 596 |
+
ENSMUSG00000081303
|
| 597 |
+
ENSMUSG00000081651
|
| 598 |
+
ENSMUSG00000081819
|
| 599 |
+
ENSMUSG00000082114
|
| 600 |
+
ENSMUSG00000082149
|
| 601 |
+
ENSMUSG00000082193
|
| 602 |
+
ENSMUSG00000082195
|
| 603 |
+
ENSMUSG00000082379
|
| 604 |
+
ENSMUSG00000082429
|
| 605 |
+
ENSMUSG00000082507
|
| 606 |
+
ENSMUSG00000082530
|
| 607 |
+
ENSMUSG00000082588
|
| 608 |
+
ENSMUSG00000082705
|
| 609 |
+
ENSMUSG00000082718
|
| 610 |
+
ENSMUSG00000082746
|
| 611 |
+
ENSMUSG00000083022
|
| 612 |
+
ENSMUSG00000083411
|
| 613 |
+
ENSMUSG00000083505
|
| 614 |
+
ENSMUSG00000083679
|
| 615 |
+
ENSMUSG00000083732
|
| 616 |
+
ENSMUSG00000083761
|
| 617 |
+
ENSMUSG00000083863
|
| 618 |
+
ENSMUSG00000083985
|
| 619 |
+
ENSMUSG00000084269
|
| 620 |
+
ENSMUSG00000084378
|
| 621 |
+
ENSMUSG00000085382
|
| 622 |
+
ENSMUSG00000085642
|
| 623 |
+
ENSMUSG00000085975
|
| 624 |
+
ENSMUSG00000086098
|
| 625 |
+
ENSMUSG00000086123
|
| 626 |
+
ENSMUSG00000086308
|
| 627 |
+
ENSMUSG00000086350
|
| 628 |
+
ENSMUSG00000086468
|
| 629 |
+
ENSMUSG00000086688
|
| 630 |
+
ENSMUSG00000086914
|
| 631 |
+
ENSMUSG00000086968
|
| 632 |
+
ENSMUSG00000086980
|
| 633 |
+
ENSMUSG00000087301
|
| 634 |
+
ENSMUSG00000087331
|
| 635 |
+
ENSMUSG00000087993
|
| 636 |
+
ENSMUSG00000089696
|
| 637 |
+
ENSMUSG00000089837
|
| 638 |
+
ENSMUSG00000090002
|
| 639 |
+
ENSMUSG00000090110
|
| 640 |
+
ENSMUSG00000090386
|
| 641 |
+
ENSMUSG00000090551
|
| 642 |
+
ENSMUSG00000090576
|
| 643 |
+
ENSMUSG00000090812
|
| 644 |
+
ENSMUSG00000091058
|
| 645 |
+
ENSMUSG00000091154
|
| 646 |
+
ENSMUSG00000091269
|
| 647 |
+
ENSMUSG00000091387
|
| 648 |
+
ENSMUSG00000091625
|
| 649 |
+
ENSMUSG00000092062
|
| 650 |
+
ENSMUSG00000092083
|
| 651 |
+
ENSMUSG00000092181
|
| 652 |
+
ENSMUSG00000092428
|
| 653 |
+
ENSMUSG00000092448
|
| 654 |
+
ENSMUSG00000092519
|
| 655 |
+
ENSMUSG00000093483
|
| 656 |
+
ENSMUSG00000093656
|
| 657 |
+
ENSMUSG00000093661
|
| 658 |
+
ENSMUSG00000093730
|
| 659 |
+
ENSMUSG00000093942
|
| 660 |
+
ENSMUSG00000094002
|
| 661 |
+
ENSMUSG00000094519
|
| 662 |
+
ENSMUSG00000094566
|
| 663 |
+
ENSMUSG00000094678
|
| 664 |
+
ENSMUSG00000094828
|
| 665 |
+
ENSMUSG00000095139
|
| 666 |
+
ENSMUSG00000095512
|
| 667 |
+
ENSMUSG00000095990
|
| 668 |
+
ENSMUSG00000096789
|
| 669 |
+
ENSMUSG00000096847
|
| 670 |
+
ENSMUSG00000096923
|
| 671 |
+
ENSMUSG00000096929
|
| 672 |
+
ENSMUSG00000097061
|
| 673 |
+
ENSMUSG00000097248
|
| 674 |
+
ENSMUSG00000097320
|
| 675 |
+
ENSMUSG00000097403
|
| 676 |
+
ENSMUSG00000097511
|
| 677 |
+
ENSMUSG00000097573
|
| 678 |
+
ENSMUSG00000097714
|
| 679 |
+
ENSMUSG00000097867
|
| 680 |
+
ENSMUSG00000097882
|
| 681 |
+
ENSMUSG00000097908
|
| 682 |
+
ENSMUSG00000097937
|
| 683 |
+
ENSMUSG00000097977
|
| 684 |
+
ENSMUSG00000098292
|
| 685 |
+
ENSMUSG00000098713
|
| 686 |
+
ENSMUSG00000098975
|
| 687 |
+
ENSMUSG00000099076
|
| 688 |
+
ENSMUSG00000099492
|
| 689 |
+
ENSMUSG00000099631
|
| 690 |
+
ENSMUSG00000099757
|
| 691 |
+
ENSMUSG00000099930
|
| 692 |
+
ENSMUSG00000100000
|
| 693 |
+
ENSMUSG00000100075
|
| 694 |
+
ENSMUSG00000100162
|
| 695 |
+
ENSMUSG00000100432
|
| 696 |
+
ENSMUSG00000100441
|
| 697 |
+
ENSMUSG00000100600
|
| 698 |
+
ENSMUSG00000100636
|
| 699 |
+
ENSMUSG00000100671
|
| 700 |
+
ENSMUSG00000100922
|
| 701 |
+
ENSMUSG00000101330
|
| 702 |
+
ENSMUSG00000101462
|
| 703 |
+
ENSMUSG00000101567
|
| 704 |
+
ENSMUSG00000101578
|
| 705 |
+
ENSMUSG00000101587
|
| 706 |
+
ENSMUSG00000101609
|
| 707 |
+
ENSMUSG00000101610
|
| 708 |
+
ENSMUSG00000101784
|
| 709 |
+
ENSMUSG00000102151
|
| 710 |
+
ENSMUSG00000102306
|
| 711 |
+
ENSMUSG00000102344
|
| 712 |
+
ENSMUSG00000102404
|
| 713 |
+
ENSMUSG00000102526
|
| 714 |
+
ENSMUSG00000102536
|
| 715 |
+
ENSMUSG00000102579
|
| 716 |
+
ENSMUSG00000102649
|
| 717 |
+
ENSMUSG00000102665
|
| 718 |
+
ENSMUSG00000102748
|
| 719 |
+
ENSMUSG00000102776
|
| 720 |
+
ENSMUSG00000103007
|
| 721 |
+
ENSMUSG00000103044
|
| 722 |
+
ENSMUSG00000103062
|
| 723 |
+
ENSMUSG00000103260
|
| 724 |
+
ENSMUSG00000103309
|
| 725 |
+
ENSMUSG00000103310
|
| 726 |
+
ENSMUSG00000103324
|
| 727 |
+
ENSMUSG00000103391
|
| 728 |
+
ENSMUSG00000103459
|
| 729 |
+
ENSMUSG00000103529
|
| 730 |
+
ENSMUSG00000103583
|
| 731 |
+
ENSMUSG00000103634
|
| 732 |
+
ENSMUSG00000103677
|
| 733 |
+
ENSMUSG00000103916
|
| 734 |
+
ENSMUSG00000103957
|
| 735 |
+
ENSMUSG00000104026
|
| 736 |
+
ENSMUSG00000104064
|
| 737 |
+
ENSMUSG00000104295
|
| 738 |
+
ENSMUSG00000104467
|
| 739 |
+
ENSMUSG00000104507
|
| 740 |
+
ENSMUSG00000104563
|
| 741 |
+
ENSMUSG00000104621
|
| 742 |
+
ENSMUSG00000104802
|
| 743 |
+
ENSMUSG00000104822
|
| 744 |
+
ENSMUSG00000105084
|
| 745 |
+
ENSMUSG00000105113
|
| 746 |
+
ENSMUSG00000105305
|
| 747 |
+
ENSMUSG00000105345
|
| 748 |
+
ENSMUSG00000105403
|
| 749 |
+
ENSMUSG00000105698
|
| 750 |
+
ENSMUSG00000105861
|
| 751 |
+
ENSMUSG00000105892
|
| 752 |
+
ENSMUSG00000105941
|
| 753 |
+
ENSMUSG00000105970
|
| 754 |
+
ENSMUSG00000105993
|
| 755 |
+
ENSMUSG00000106044
|
| 756 |
+
ENSMUSG00000106189
|
| 757 |
+
ENSMUSG00000106262
|
| 758 |
+
ENSMUSG00000106427
|
| 759 |
+
ENSMUSG00000106515
|
| 760 |
+
ENSMUSG00000106735
|
| 761 |
+
ENSMUSG00000106747
|
| 762 |
+
ENSMUSG00000106818
|
| 763 |
+
ENSMUSG00000106868
|
| 764 |
+
ENSMUSG00000106992
|
| 765 |
+
ENSMUSG00000107035
|
| 766 |
+
ENSMUSG00000107219
|
| 767 |
+
ENSMUSG00000107760
|
| 768 |
+
ENSMUSG00000107909
|
| 769 |
+
ENSMUSG00000108053
|
| 770 |
+
ENSMUSG00000108105
|
| 771 |
+
ENSMUSG00000108199
|
| 772 |
+
ENSMUSG00000108211
|
| 773 |
+
ENSMUSG00000108291
|
| 774 |
+
ENSMUSG00000108297
|
| 775 |
+
ENSMUSG00000108443
|
| 776 |
+
ENSMUSG00000108551
|
| 777 |
+
ENSMUSG00000108658
|
| 778 |
+
ENSMUSG00000108776
|
| 779 |
+
ENSMUSG00000108804
|
| 780 |
+
ENSMUSG00000108892
|
| 781 |
+
ENSMUSG00000109044
|
| 782 |
+
ENSMUSG00000109108
|
| 783 |
+
ENSMUSG00000109118
|
| 784 |
+
ENSMUSG00000109206
|
| 785 |
+
ENSMUSG00000109231
|
| 786 |
+
ENSMUSG00000109427
|
| 787 |
+
ENSMUSG00000109549
|
| 788 |
+
ENSMUSG00000109636
|
| 789 |
+
ENSMUSG00000109679
|
| 790 |
+
ENSMUSG00000109710
|
| 791 |
+
ENSMUSG00000109865
|
| 792 |
+
ENSMUSG00000109887
|
| 793 |
+
ENSMUSG00000109946
|
| 794 |
+
ENSMUSG00000110030
|
| 795 |
+
ENSMUSG00000110044
|
| 796 |
+
ENSMUSG00000110191
|
| 797 |
+
ENSMUSG00000110236
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/entrez_3xTgAD.txt
ADDED
|
@@ -0,0 +1,485 @@
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| 471 |
+
628686
|
| 472 |
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320879
|
| 473 |
+
100042074
|
| 474 |
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674597
|
| 475 |
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77741
|
| 476 |
+
67325
|
| 477 |
+
13924
|
| 478 |
+
211429
|
| 479 |
+
68982
|
| 480 |
+
433466
|
| 481 |
+
102466790
|
| 482 |
+
102465790
|
| 483 |
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102634738
|
| 484 |
+
667759
|
| 485 |
+
102633582
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/entrez_PS3O1S.txt
ADDED
|
@@ -0,0 +1,633 @@
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|
| 1 |
+
231841
|
| 2 |
+
14395
|
| 3 |
+
14667
|
| 4 |
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12727
|
| 5 |
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20302
|
| 6 |
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224897
|
| 7 |
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433864
|
| 8 |
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24109
|
| 9 |
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27060
|
| 10 |
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232670
|
| 11 |
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66877
|
| 12 |
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66917
|
| 13 |
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227720
|
| 14 |
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20514
|
| 15 |
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71887
|
| 16 |
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57875
|
| 17 |
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13549
|
| 18 |
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58175
|
| 19 |
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21803
|
| 20 |
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68079
|
| 21 |
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14231
|
| 22 |
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83435
|
| 23 |
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70209
|
| 24 |
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399566
|
| 25 |
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66174
|
| 26 |
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67846
|
| 27 |
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11772
|
| 28 |
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11767
|
| 29 |
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14773
|
| 30 |
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59287
|
| 31 |
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12308
|
| 32 |
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67619
|
| 33 |
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67030
|
| 34 |
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19156
|
| 35 |
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53417
|
| 36 |
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52535
|
| 37 |
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110826
|
| 38 |
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20511
|
| 39 |
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56384
|
| 40 |
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20513
|
| 41 |
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56513
|
| 42 |
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13476
|
| 43 |
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66989
|
| 44 |
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69660
|
| 45 |
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15216
|
| 46 |
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71472
|
| 47 |
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18771
|
| 48 |
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72611
|
| 49 |
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15257
|
| 50 |
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56455
|
| 51 |
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192650
|
| 52 |
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286942
|
| 53 |
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56395
|
| 54 |
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63872
|
| 55 |
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320938
|
| 56 |
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27883
|
| 57 |
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19378
|
| 58 |
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67979
|
| 59 |
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21766
|
| 60 |
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27362
|
| 61 |
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74154
|
| 62 |
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20933
|
| 63 |
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16803
|
| 64 |
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12946
|
| 65 |
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76366
|
| 66 |
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271305
|
| 67 |
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18803
|
| 68 |
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52469
|
| 69 |
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|
| 70 |
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22032
|
| 71 |
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59040
|
| 72 |
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109754
|
| 73 |
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54401
|
| 74 |
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71774
|
| 75 |
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22658
|
| 76 |
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68729
|
| 77 |
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12921
|
| 78 |
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12514
|
| 79 |
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19340
|
| 80 |
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68267
|
| 81 |
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353499
|
| 82 |
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108853
|
| 83 |
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103213
|
| 84 |
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170728
|
| 85 |
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52713
|
| 86 |
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16773
|
| 87 |
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52696
|
| 88 |
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20393
|
| 89 |
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56422
|
| 90 |
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216344
|
| 91 |
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11540
|
| 92 |
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30055
|
| 93 |
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50493
|
| 94 |
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75530
|
| 95 |
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15525
|
| 96 |
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74563
|
| 97 |
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16886
|
| 98 |
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71853
|
| 99 |
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71916
|
| 100 |
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12033
|
| 101 |
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104111
|
| 102 |
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13382
|
| 103 |
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11421
|
| 104 |
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217333
|
| 105 |
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21689
|
| 106 |
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98238
|
| 107 |
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13385
|
| 108 |
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75689
|
| 109 |
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217666
|
| 110 |
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217737
|
| 111 |
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104886
|
| 112 |
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110417
|
| 113 |
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108760
|
| 114 |
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27277
|
| 115 |
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22632
|
| 116 |
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76137
|
| 117 |
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72935
|
| 118 |
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212483
|
| 119 |
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72562
|
| 120 |
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218397
|
| 121 |
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218461
|
| 122 |
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15550
|
| 123 |
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59007
|
| 124 |
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70561
|
| 125 |
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11744
|
| 126 |
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50769
|
| 127 |
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18826
|
| 128 |
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22380
|
| 129 |
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13449
|
| 130 |
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76355
|
| 131 |
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76338
|
| 132 |
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219072
|
| 133 |
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319984
|
| 134 |
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67819
|
| 135 |
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21685
|
| 136 |
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20524
|
| 137 |
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20972
|
| 138 |
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74158
|
| 139 |
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19230
|
| 140 |
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13731
|
| 141 |
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66049
|
| 142 |
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17069
|
| 143 |
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12651
|
| 144 |
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70508
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
| 632 |
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|
| 633 |
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115486941
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/execution_log.txt
ADDED
|
@@ -0,0 +1,2106 @@
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|
| 1 |
+
================================ Human Message =================================
|
| 2 |
+
|
| 3 |
+
You are running a bioagent-bench task with local files already prepared.
|
| 4 |
+
|
| 5 |
+
Task ID: alzheimer-mouse
|
| 6 |
+
Task name: Alzheimer Mouse Models: Comparative Pathway Analysis
|
| 7 |
+
Benchmark prompt:
|
| 8 |
+
Perform a comparative differential expression analysis of three different Alzheimer's Disease mouse models (5xFAD, 3xTG-AD, and PS3O1S) to identify shared molecular KEGG pathways. The output should be a CSV file with the following columns: 'pathway','5xFAD_pvalue','3xTG_AD_pvalue','PS3O1S_pvalue'. Example csv <example>Pathway,5xFAD_pvalue,3xTG_AD_pvalue,PS3O1S_pvalue
|
| 9 |
+
Phagosome Homo sapiens hsa04145,1.5045916403148935e-09,0.3102788532065793,0.4443015705596512
|
| 10 |
+
</example>
|
| 11 |
+
Data background:
|
| 12 |
+
Analyze 5xFAD, 3xTG-AD, and PS301S mouse models: normalize counts, perform differential expression, run KEGG pathway enrichment, and compare shared pathways across models.
|
| 13 |
+
|
| 14 |
+
Constraints:
|
| 15 |
+
1. Use only the benchmark inputs and references explicitly listed below.
|
| 16 |
+
2. Save the required final deliverables exactly to the paths listed below.
|
| 17 |
+
3. Save all intermediate scripts, logs, and scratch outputs inside this run directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905
|
| 18 |
+
4. Keep final deliverables in the same schema/format requested by the benchmark prompt.
|
| 19 |
+
5. Return a concise final summary after writing the required files.
|
| 20 |
+
|
| 21 |
+
Task-specific instruction:
|
| 22 |
+
Use the provided mouse count and DEA files as inputs. Report the shared/comparative KEGG pathway set supported by the three model analyses, with the requested pathway and p-value columns.
|
| 23 |
+
|
| 24 |
+
Benchmark data policy:
|
| 25 |
+
- Allowed input data directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data
|
| 26 |
+
- Allowed reference directory: <none>
|
| 27 |
+
- Allowed scratch/output directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905
|
| 28 |
+
- Forbidden truth/results directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/results
|
| 29 |
+
- Forbidden sibling benchmark task directories: /225040511/project/bioagent-bench/dataset/<any task other than alzheimer-mouse>
|
| 30 |
+
- Do not inspect previous bioagent-bench-runs or sibling task outputs as data sources.
|
| 31 |
+
- Do not download external databases or install new packages during the benchmark run.
|
| 32 |
+
|
| 33 |
+
Input data directory:
|
| 34 |
+
/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data
|
| 35 |
+
Visible input files:
|
| 36 |
+
- DEA_PS3O1S.csv
|
| 37 |
+
- GSE161904_Raw_gene_counts_cortex.txt
|
| 38 |
+
- GSE168137_countList.txt
|
| 39 |
+
|
| 40 |
+
Reference data directory:
|
| 41 |
+
<none>
|
| 42 |
+
Visible reference files:
|
| 43 |
+
- <none>
|
| 44 |
+
|
| 45 |
+
Required final output paths:
|
| 46 |
+
- pathway_comparison.csv: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv
|
| 47 |
+
|
| 48 |
+
================================== Ai Message ==================================
|
| 49 |
+
|
| 50 |
+
I'll start by examining the input data files to understand their structure and content.
|
| 51 |
+
|
| 52 |
+
**Plan:**
|
| 53 |
+
1. [ ] Explore the input data directory and examine the structure of each file
|
| 54 |
+
2. [ ] Determine which files correspond to which mouse models
|
| 55 |
+
3. [ ] Perform differential expression analysis for models where raw counts are available
|
| 56 |
+
4. [ ] Run KEGG pathway enrichment analysis for each model
|
| 57 |
+
5. [ ] Combine the results into the required CSV format
|
| 58 |
+
|
| 59 |
+
Let me begin.
|
| 60 |
+
|
| 61 |
+
<execute>
|
| 62 |
+
#!BASH
|
| 63 |
+
echo "=== Listing input data directory ==="
|
| 64 |
+
ls -la /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/
|
| 65 |
+
echo ""
|
| 66 |
+
echo "=== Checking file sizes ==="
|
| 67 |
+
wc -l /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/*
|
| 68 |
+
echo ""
|
| 69 |
+
echo "=== First few lines of each file ==="
|
| 70 |
+
echo "--- DEA_PS3O1S.csv ---"
|
| 71 |
+
head -5 /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/DEA_PS3O1S.csv
|
| 72 |
+
echo ""
|
| 73 |
+
echo "--- GSE161904_Raw_gene_counts_cortex.txt ---"
|
| 74 |
+
head -5 /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/GSE161904_Raw_gene_counts_cortex.txt
|
| 75 |
+
echo ""
|
| 76 |
+
echo "--- GSE168137_countList.txt ---"
|
| 77 |
+
head -5 /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/GSE168137_countList.txt
|
| 78 |
+
</execute>
|
| 79 |
+
|
| 80 |
+
================================== Ai Message ==================================
|
| 81 |
+
|
| 82 |
+
<observation>=== Listing input data directory ===
|
| 83 |
+
total 12097
|
| 84 |
+
drwxr-xr-x 2 root root 4096 May 13 10:10 .
|
| 85 |
+
drwxr-xr-x 4 root root 4096 May 14 16:36 ..
|
| 86 |
+
-rw-r--r-- 1 1000 1000 6338318 May 25 2025 DEA_PS3O1S.csv
|
| 87 |
+
-rw-r--r-- 1 1000 1000 1622885 May 25 2025 GSE161904_Raw_gene_counts_cortex.txt
|
| 88 |
+
-rw-r--r-- 1 1000 1000 4388517 May 25 2025 GSE168137_countList.txt
|
| 89 |
+
|
| 90 |
+
=== Checking file sizes ===
|
| 91 |
+
48527 /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/DEA_PS3O1S.csv
|
| 92 |
+
43630 /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/GSE161904_Raw_gene_counts_cortex.txt
|
| 93 |
+
55450 /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/GSE168137_countList.txt
|
| 94 |
+
147607 total
|
| 95 |
+
|
| 96 |
+
=== First few lines of each file ===
|
| 97 |
+
--- DEA_PS3O1S.csv ---
|
| 98 |
+
,gene_id,gene_name,feature,fc,log2fc,pval,qval,wt.MeanFPKM,tg.MeanFPKM,FPKM.tau_02,FPKM.tau_03,FPKM.tau_04,FPKM.tau_01,FPKM.tau_05,FPKM.tau_06
|
| 99 |
+
1,ENSMUSG00000000001,Gnai3,gene,1.06747898228474,0.0942076647384222,0.60011587383902,0.899032601644565,8.61282333333333,9.080672,8.667066,9.120558,8.050846,10.898668,7.448256,8.895092
|
| 100 |
+
2,ENSMUSG00000000003,Pbsn,gene,1.0,0.0,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
|
| 101 |
+
3,ENSMUSG00000000028,Cdc45,gene,1.0,0.0,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
|
| 102 |
+
4,ENSMUSG00000000031,H19,gene,1.0,0.0,,,0.0,0.0,0.0,0.0,0.0,0.0,0.0,0.0
|
| 103 |
+
|
| 104 |
+
--- GSE161904_Raw_gene_counts_cortex.txt ---
|
| 105 |
+
G3R1_Cortex_3xTgAD G3R3_Cortex_3xTgAD G3R4_Cortex_3xTgAD G3R10_Cortex_WT G3R7_Cortex_WT G3R9_Cortex_WT
|
| 106 |
+
ENSMUSG00000000001 1020 1095 1203 1225 1116 1106
|
| 107 |
+
ENSMUSG00000000003 0 0 0 0 0 0
|
| 108 |
+
ENSMUSG00000000028 63 77 59 90 69 97
|
| 109 |
+
ENSMUSG00000000031 3 0 3 0 2 1
|
| 110 |
+
|
| 111 |
+
--- GSE168137_countList.txt ---
|
| 112 |
+
gene_id 5xFAD;BL6_cortex_8mon_Female_295 5xFAD;BL6_cortex_8mon_Female_312 5xFAD;BL6_cortex_8mon_Female_339 5xFAD;BL6_cortex_8mon_Female_341 5xFAD;BL6_cortex_8mon_Female_342 5xFAD;BL6_cortex_8mon_Male_299 5xFAD;BL6_cortex_8mon_Male_300 5xFAD;BL6_cortex_8mon_Male_307 5xFAD;BL6_cortex_8mon_Male_387 5xFAD;BL6_cortex_8mon_Male_390 BL6_cortex_8mon_Female_322 BL6_cortex_8mon_Female_338 BL6_cortex_8mon_Female_340 BL6_cortex_8mon_Female_348 BL6_cortex_8mon_Female_351 BL6_cortex_8mon_Male_389 BL6_cortex_8mon_Male_396 BL6_cortex_8mon_Male_399 BL6_cortex_8mon_Male_410 BL6_cortex_8mon_Male_412
|
| 113 |
+
ENSMUSG00000000001.4 729 614 610 614 484 613 607 393 645 339 465 497 673 396 500 711 325 777 837 670
|
| 114 |
+
ENSMUSG00000000003.15 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
| 115 |
+
ENSMUSG00000000028.15 21 38 31 35 19 40 34 23 34 19 28 25 34 23 32 29 15 44 36 24
|
| 116 |
+
ENSMUSG00000000031.16 4 4 0 0 1 2 0 0 0 0 0 0 2 1 1 5 1 1 0 2
|
| 117 |
+
</observation>
|
| 118 |
+
|
| 119 |
+
================================== Ai Message ==================================
|
| 120 |
+
|
| 121 |
+
Now I understand the data structure. Let me examine the data more closely.
|
| 122 |
+
|
| 123 |
+
<execute>
|
| 124 |
+
#!BASH
|
| 125 |
+
echo "=== PS3O1S DEA columns ==="
|
| 126 |
+
head -1 /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/DEA_PS3O1S.csv | tr ',' '\n' | cat -n
|
| 127 |
+
echo ""
|
| 128 |
+
echo "=== 3xTg-AD file columns ==="
|
| 129 |
+
head -1 /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/GSE161904_Raw_gene_counts_cortex.txt | tr '\t' '\n' | cat -n
|
| 130 |
+
echo ""
|
| 131 |
+
echo "=== 5xFAD file columns ==="
|
| 132 |
+
head -1 /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/GSE168137_countList.txt | tr '\t' '\n' | cat -n
|
| 133 |
+
</execute>
|
| 134 |
+
|
| 135 |
+
================================== Ai Message ==================================
|
| 136 |
+
|
| 137 |
+
<observation>=== PS3O1S DEA columns ===
|
| 138 |
+
1
|
| 139 |
+
2 gene_id
|
| 140 |
+
3 gene_name
|
| 141 |
+
4 feature
|
| 142 |
+
5 fc
|
| 143 |
+
6 log2fc
|
| 144 |
+
7 pval
|
| 145 |
+
8 qval
|
| 146 |
+
9 wt.MeanFPKM
|
| 147 |
+
10 tg.MeanFPKM
|
| 148 |
+
11 FPKM.tau_02
|
| 149 |
+
12 FPKM.tau_03
|
| 150 |
+
13 FPKM.tau_04
|
| 151 |
+
14 FPKM.tau_01
|
| 152 |
+
15 FPKM.tau_05
|
| 153 |
+
16 FPKM.tau_06
|
| 154 |
+
|
| 155 |
+
=== 3xTg-AD file columns ===
|
| 156 |
+
1
|
| 157 |
+
2 G3R1_Cortex_3xTgAD
|
| 158 |
+
3 G3R3_Cortex_3xTgAD
|
| 159 |
+
4 G3R4_Cortex_3xTgAD
|
| 160 |
+
5 G3R10_Cortex_WT
|
| 161 |
+
6 G3R7_Cortex_WT
|
| 162 |
+
7 G3R9_Cortex_WT
|
| 163 |
+
|
| 164 |
+
=== 5xFAD file columns ===
|
| 165 |
+
1 gene_id
|
| 166 |
+
2 5xFAD;BL6_cortex_8mon_Female_295
|
| 167 |
+
3 5xFAD;BL6_cortex_8mon_Female_312
|
| 168 |
+
4 5xFAD;BL6_cortex_8mon_Female_339
|
| 169 |
+
5 5xFAD;BL6_cortex_8mon_Female_341
|
| 170 |
+
6 5xFAD;BL6_cortex_8mon_Female_342
|
| 171 |
+
7 5xFAD;BL6_cortex_8mon_Male_299
|
| 172 |
+
8 5xFAD;BL6_cortex_8mon_Male_300
|
| 173 |
+
9 5xFAD;BL6_cortex_8mon_Male_307
|
| 174 |
+
10 5xFAD;BL6_cortex_8mon_Male_387
|
| 175 |
+
11 5xFAD;BL6_cortex_8mon_Male_390
|
| 176 |
+
12 BL6_cortex_8mon_Female_322
|
| 177 |
+
13 BL6_cortex_8mon_Female_338
|
| 178 |
+
14 BL6_cortex_8mon_Female_340
|
| 179 |
+
15 BL6_cortex_8mon_Female_348
|
| 180 |
+
16 BL6_cortex_8mon_Female_351
|
| 181 |
+
17 BL6_cortex_8mon_Male_389
|
| 182 |
+
18 BL6_cortex_8mon_Male_396
|
| 183 |
+
19 BL6_cortex_8mon_Male_399
|
| 184 |
+
20 BL6_cortex_8mon_Male_410
|
| 185 |
+
21 BL6_cortex_8mon_Male_412
|
| 186 |
+
</observation>
|
| 187 |
+
|
| 188 |
+
================================ Human Message =================================
|
| 189 |
+
|
| 190 |
+
Each response must include thinking process followed by either <execute> or <solution> tag. But there are no tags in the current response. Please follow the instruction, fix and regenerate the response again.
|
| 191 |
+
|
| 192 |
+
================================ Human Message =================================
|
| 193 |
+
|
| 194 |
+
Each response must include thinking process followed by either <execute> or <solution> tag. But there are no tags in the current response. Please follow the instruction, fix and regenerate the response again.
|
| 195 |
+
|
| 196 |
+
================================== Ai Message ==================================
|
| 197 |
+
|
| 198 |
+
You're right, I apologize for the missing tags. Let me proceed properly with the analysis.
|
| 199 |
+
|
| 200 |
+
**Plan:**
|
| 201 |
+
1. [ ] Examine the data and prepare count files and metadata for each mouse model
|
| 202 |
+
2. [ ] Run DESeq2 for 5xFAD model (GSE168137)
|
| 203 |
+
3. [ ] Run DESeq2 for 3xTg-AD model (GSE161904)
|
| 204 |
+
4. [ ] Use pre-computed DEA for PS3O1S
|
| 205 |
+
5. [ ] Convert gene IDs to Entrez for KEGG enrichment
|
| 206 |
+
6. [ ] Run KEGG enrichment for all three models
|
| 207 |
+
7. [ ] Combine results into final CSV with shared pathways
|
| 208 |
+
|
| 209 |
+
Let me start by preparing the data files and examining gene IDs.
|
| 210 |
+
|
| 211 |
+
<execute>
|
| 212 |
+
#!BASH
|
| 213 |
+
echo "=== Checking gene ID format in 5xFAD ==="
|
| 214 |
+
head -3 /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/GSE168137_countList.txt | cut -f1
|
| 215 |
+
echo ""
|
| 216 |
+
echo "=== Checking gene ID format in 3xTg-AD ==="
|
| 217 |
+
head -3 /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/GSE161904_Raw_gene_counts_cortex.txt | cut -f1
|
| 218 |
+
echo ""
|
| 219 |
+
echo "=== Checking gene ID format in PS3O1S ==="
|
| 220 |
+
head -3 /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/DEA_PS3O1S.csv | cut -d',' -f2,3
|
| 221 |
+
</execute>
|
| 222 |
+
|
| 223 |
+
================================== Ai Message ==================================
|
| 224 |
+
|
| 225 |
+
<observation>=== Checking gene ID format in 5xFAD ===
|
| 226 |
+
gene_id
|
| 227 |
+
ENSMUSG00000000001.4
|
| 228 |
+
ENSMUSG00000000003.15
|
| 229 |
+
|
| 230 |
+
=== Checking gene ID format in 3xTg-AD ===
|
| 231 |
+
|
| 232 |
+
ENSMUSG00000000001
|
| 233 |
+
ENSMUSG00000000003
|
| 234 |
+
|
| 235 |
+
=== Checking gene ID format in PS3O1S ===
|
| 236 |
+
gene_id,gene_name
|
| 237 |
+
ENSMUSG00000000001,Gnai3
|
| 238 |
+
ENSMUSG00000000003,Pbsn
|
| 239 |
+
</observation>
|
| 240 |
+
|
| 241 |
+
================================== Ai Message ==================================
|
| 242 |
+
|
| 243 |
+
<execute>
|
| 244 |
+
#!BASH
|
| 245 |
+
echo "Step 1: Prepare count files and metadata for DESeq2 analysis"
|
| 246 |
+
|
| 247 |
+
cd /225040511/project/biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905
|
| 248 |
+
|
| 249 |
+
# Prepare 5xFAD count matrix - separate counts from metadata
|
| 250 |
+
echo "Preparing 5xFAD count matrix..."
|
| 251 |
+
python3 -c "
|
| 252 |
+
import pandas as pd
|
| 253 |
+
|
| 254 |
+
# Read 5xFAD data
|
| 255 |
+
df = pd.read_csv('/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/GSE168137_countList.txt', sep='\t')
|
| 256 |
+
# Clean gene IDs (remove .version suffix)
|
| 257 |
+
df['gene_id'] = df['gene_id'].str.replace(r'\..*$', '', regex=True)
|
| 258 |
+
df = df.set_index('gene_id')
|
| 259 |
+
|
| 260 |
+
# Separate 5xFAD (TG) and BL6 (WT) samples
|
| 261 |
+
tg_cols = [c for c in df.columns if c.startswith('5xFAD')]
|
| 262 |
+
wt_cols = [c for c in df.columns if c.startswith('BL6')]
|
| 263 |
+
|
| 264 |
+
print(f'5xFAD TG samples: {len(tg_cols)}')
|
| 265 |
+
print(f'5xFAD WT samples: {len(wt_cols)}')
|
| 266 |
+
print(f'TG cols: {tg_cols}')
|
| 267 |
+
print(f'WT cols: {wt_cols}')
|
| 268 |
+
|
| 269 |
+
# Create count matrix
|
| 270 |
+
counts_5xfad = df[tg_cols + wt_cols]
|
| 271 |
+
counts_5xfad.to_csv('counts_5xFAD.csv')
|
| 272 |
+
print(f'Count matrix shape: {counts_5xfad.shape}')
|
| 273 |
+
|
| 274 |
+
# Create metadata
|
| 275 |
+
metadata_5xfad = pd.DataFrame({
|
| 276 |
+
'sample': tg_cols + wt_cols,
|
| 277 |
+
'condition': ['5xFAD']*len(tg_cols) + ['WT']*len(wt_cols)
|
| 278 |
+
})
|
| 279 |
+
metadata_5xfad.to_csv('metadata_5xFAD.csv', index=False)
|
| 280 |
+
print(metadata_5xfad)
|
| 281 |
+
"
|
| 282 |
+
</execute>
|
| 283 |
+
|
| 284 |
+
================================== Ai Message ==================================
|
| 285 |
+
|
| 286 |
+
<observation>Error running Bash script (exit code 1):
|
| 287 |
+
/tmp/tmptg2j8c9m.sh: line 6: cd: /225040511/project/biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905: No such file or directory
|
| 288 |
+
</observation>
|
| 289 |
+
|
| 290 |
+
================================== Ai Message ==================================
|
| 291 |
+
|
| 292 |
+
<execute>
|
| 293 |
+
#!BASH
|
| 294 |
+
echo "Step 1: Prepare count files and metadata for DESeq2 analysis"
|
| 295 |
+
|
| 296 |
+
cd /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905
|
| 297 |
+
|
| 298 |
+
# Prepare 5xFAD count matrix - separate counts from metadata
|
| 299 |
+
echo "Preparing 5xFAD count matrix..."
|
| 300 |
+
python3 -c "
|
| 301 |
+
import pandas as pd
|
| 302 |
+
|
| 303 |
+
# Read 5xFAD data
|
| 304 |
+
df = pd.read_csv('/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/GSE168137_countList.txt', sep='\t')
|
| 305 |
+
# Clean gene IDs (remove .version suffix)
|
| 306 |
+
df['gene_id'] = df['gene_id'].str.replace(r'\..*$', '', regex=True)
|
| 307 |
+
df = df.set_index('gene_id')
|
| 308 |
+
|
| 309 |
+
# Separate 5xFAD (TG) and BL6 (WT) samples
|
| 310 |
+
tg_cols = [c for c in df.columns if c.startswith('5xFAD')]
|
| 311 |
+
wt_cols = [c for c in df.columns if c.startswith('BL6')]
|
| 312 |
+
|
| 313 |
+
print(f'5xFAD TG samples: {len(tg_cols)}')
|
| 314 |
+
print(f'5xFAD WT samples: {len(wt_cols)}')
|
| 315 |
+
print(f'TG cols: {tg_cols}')
|
| 316 |
+
print(f'WT cols: {wt_cols}')
|
| 317 |
+
|
| 318 |
+
# Create count matrix
|
| 319 |
+
counts_5xfad = df[tg_cols + wt_cols]
|
| 320 |
+
counts_5xfad.to_csv('counts_5xFAD.csv')
|
| 321 |
+
print(f'Count matrix shape: {counts_5xfad.shape}')
|
| 322 |
+
|
| 323 |
+
# Create metadata
|
| 324 |
+
metadata_5xfad = pd.DataFrame({
|
| 325 |
+
'sample': tg_cols + wt_cols,
|
| 326 |
+
'condition': ['5xFAD']*len(tg_cols) + ['WT']*len(wt_cols)
|
| 327 |
+
})
|
| 328 |
+
metadata_5xfad.to_csv('metadata_5xFAD.csv', index=False)
|
| 329 |
+
print(metadata_5xfad)
|
| 330 |
+
"
|
| 331 |
+
</execute>
|
| 332 |
+
|
| 333 |
+
================================== Ai Message ==================================
|
| 334 |
+
|
| 335 |
+
<observation>Step 1: Prepare count files and metadata for DESeq2 analysis
|
| 336 |
+
Preparing 5xFAD count matrix...
|
| 337 |
+
5xFAD TG samples: 10
|
| 338 |
+
5xFAD WT samples: 10
|
| 339 |
+
TG cols: ['5xFAD;BL6_cortex_8mon_Female_295', '5xFAD;BL6_cortex_8mon_Female_312', '5xFAD;BL6_cortex_8mon_Female_339', '5xFAD;BL6_cortex_8mon_Female_341', '5xFAD;BL6_cortex_8mon_Female_342', '5xFAD;BL6_cortex_8mon_Male_299', '5xFAD;BL6_cortex_8mon_Male_300', '5xFAD;BL6_cortex_8mon_Male_307', '5xFAD;BL6_cortex_8mon_Male_387', '5xFAD;BL6_cortex_8mon_Male_390']
|
| 340 |
+
WT cols: ['BL6_cortex_8mon_Female_322', 'BL6_cortex_8mon_Female_338', 'BL6_cortex_8mon_Female_340', 'BL6_cortex_8mon_Female_348', 'BL6_cortex_8mon_Female_351', 'BL6_cortex_8mon_Male_389', 'BL6_cortex_8mon_Male_396', 'BL6_cortex_8mon_Male_399', 'BL6_cortex_8mon_Male_410', 'BL6_cortex_8mon_Male_412']
|
| 341 |
+
Count matrix shape: (55449, 20)
|
| 342 |
+
sample condition
|
| 343 |
+
0 5xFAD;BL6_cortex_8mon_Female_295 5xFAD
|
| 344 |
+
1 5xFAD;BL6_cortex_8mon_Female_312 5xFAD
|
| 345 |
+
2 5xFAD;BL6_cortex_8mon_Female_339 5xFAD
|
| 346 |
+
3 5xFAD;BL6_cortex_8mon_Female_341 5xFAD
|
| 347 |
+
4 5xFAD;BL6_cortex_8mon_Female_342 5xFAD
|
| 348 |
+
5 5xFAD;BL6_cortex_8mon_Male_299 5xFAD
|
| 349 |
+
6 5xFAD;BL6_cortex_8mon_Male_300 5xFAD
|
| 350 |
+
7 5xFAD;BL6_cortex_8mon_Male_307 5xFAD
|
| 351 |
+
8 5xFAD;BL6_cortex_8mon_Male_387 5xFAD
|
| 352 |
+
9 5xFAD;BL6_cortex_8mon_Male_390 5xFAD
|
| 353 |
+
10 BL6_cortex_8mon_Female_322 WT
|
| 354 |
+
11 BL6_cortex_8mon_Female_338 WT
|
| 355 |
+
12 BL6_cortex_8mon_Female_340 WT
|
| 356 |
+
13 BL6_cortex_8mon_Female_348 WT
|
| 357 |
+
14 BL6_cortex_8mon_Female_351 WT
|
| 358 |
+
15 BL6_cortex_8mon_Male_389 WT
|
| 359 |
+
16 BL6_cortex_8mon_Male_396 WT
|
| 360 |
+
17 BL6_cortex_8mon_Male_399 WT
|
| 361 |
+
18 BL6_cortex_8mon_Male_410 WT
|
| 362 |
+
19 BL6_cortex_8mon_Male_412 WT
|
| 363 |
+
</observation>
|
| 364 |
+
|
| 365 |
+
================================== Ai Message ==================================
|
| 366 |
+
|
| 367 |
+
Now let me prepare the 3xTg-AD data.
|
| 368 |
+
|
| 369 |
+
<execute>
|
| 370 |
+
#!BASH
|
| 371 |
+
echo "Preparing 3xTg-AD count matrix..."
|
| 372 |
+
cd /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905
|
| 373 |
+
|
| 374 |
+
python3 -c "
|
| 375 |
+
import pandas as pd
|
| 376 |
+
|
| 377 |
+
# Read 3xTg-AD data
|
| 378 |
+
df = pd.read_csv('/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/GSE161904_Raw_gene_counts_cortex.txt', sep='\t')
|
| 379 |
+
print(f'Raw shape: {df.shape}')
|
| 380 |
+
print(f'Columns: {df.columns.tolist()}')
|
| 381 |
+
print(df.head(3))
|
| 382 |
+
"
|
| 383 |
+
</execute>
|
| 384 |
+
|
| 385 |
+
================================== Ai Message ==================================
|
| 386 |
+
|
| 387 |
+
<observation>Preparing 3xTg-AD count matrix...
|
| 388 |
+
Raw shape: (43629, 7)
|
| 389 |
+
Columns: ['Unnamed: 0', 'G3R1_Cortex_3xTgAD', 'G3R3_Cortex_3xTgAD', 'G3R4_Cortex_3xTgAD', 'G3R10_Cortex_WT', 'G3R7_Cortex_WT', 'G3R9_Cortex_WT']
|
| 390 |
+
Unnamed: 0 G3R1_Cortex_3xTgAD ... G3R7_Cortex_WT G3R9_Cortex_WT
|
| 391 |
+
0 ENSMUSG00000000001 1020 ... 1116 1106
|
| 392 |
+
1 ENSMUSG00000000003 0 ... 0 0
|
| 393 |
+
2 ENSMUSG00000000028 63 ... 69 97
|
| 394 |
+
|
| 395 |
+
[3 rows x 7 columns]
|
| 396 |
+
</observation>
|
| 397 |
+
|
| 398 |
+
================================== Ai Message ==================================
|
| 399 |
+
|
| 400 |
+
Now let me prepare the 3xTg-AD data and then run DESeq2.
|
| 401 |
+
|
| 402 |
+
<execute>
|
| 403 |
+
#!BASH
|
| 404 |
+
echo "Preparing 3xTg-AD count matrix and metadata..."
|
| 405 |
+
cd /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905
|
| 406 |
+
|
| 407 |
+
python3 -c "
|
| 408 |
+
import pandas as pd
|
| 409 |
+
|
| 410 |
+
# Read 3xTg-AD data
|
| 411 |
+
df = pd.read_csv('/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/GSE161904_Raw_gene_counts_cortex.txt', sep='\t')
|
| 412 |
+
df = df.rename(columns={'Unnamed: 0': 'gene_id'})
|
| 413 |
+
df = df.set_index('gene_id')
|
| 414 |
+
|
| 415 |
+
# 3xTg-AD samples and WT samples
|
| 416 |
+
tg_cols = [c for c in df.columns if '3xTgAD' in c]
|
| 417 |
+
wt_cols = [c for c in df.columns if 'WT' in c]
|
| 418 |
+
|
| 419 |
+
print(f'3xTg-AD TG samples: {tg_cols}')
|
| 420 |
+
print(f'3xTg-AD WT samples: {wt_cols}')
|
| 421 |
+
|
| 422 |
+
counts_3xtg = df[tg_cols + wt_cols]
|
| 423 |
+
counts_3xtg.to_csv('counts_3xTgAD.csv')
|
| 424 |
+
print(f'Count matrix shape: {counts_3xtg.shape}')
|
| 425 |
+
|
| 426 |
+
# Create metadata
|
| 427 |
+
metadata_3xtg = pd.DataFrame({
|
| 428 |
+
'sample': tg_cols + wt_cols,
|
| 429 |
+
'condition': ['3xTgAD']*len(tg_cols) + ['WT']*len(wt_cols)
|
| 430 |
+
})
|
| 431 |
+
metadata_3xtg.to_csv('metadata_3xTgAD.csv', index=False)
|
| 432 |
+
print(metadata_3xtg)
|
| 433 |
+
"
|
| 434 |
+
|
| 435 |
+
echo ""
|
| 436 |
+
echo "Preparing PS3O1S DEA genes..."
|
| 437 |
+
python3 -c "
|
| 438 |
+
import pandas as pd
|
| 439 |
+
|
| 440 |
+
# Read PS3O1S DEA
|
| 441 |
+
df = pd.read_csv('/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/DEA_PS3O1S.csv', index_col=0)
|
| 442 |
+
print(f'PS3O1S DEA shape: {df.shape}')
|
| 443 |
+
print(f'Columns: {df.columns.tolist()}')
|
| 444 |
+
print(f'Number of genes with pval: {df[\"pval\"].notna().sum()}')
|
| 445 |
+
print(f'Top genes:')
|
| 446 |
+
print(df.sort_values('pval').head(10))
|
| 447 |
+
"
|
| 448 |
+
</execute>
|
| 449 |
+
|
| 450 |
+
================================== Ai Message ==================================
|
| 451 |
+
|
| 452 |
+
<observation>Preparing 3xTg-AD count matrix and metadata...
|
| 453 |
+
3xTg-AD TG samples: ['G3R1_Cortex_3xTgAD', 'G3R3_Cortex_3xTgAD', 'G3R4_Cortex_3xTgAD']
|
| 454 |
+
3xTg-AD WT samples: ['G3R10_Cortex_WT', 'G3R7_Cortex_WT', 'G3R9_Cortex_WT']
|
| 455 |
+
Count matrix shape: (43629, 6)
|
| 456 |
+
sample condition
|
| 457 |
+
0 G3R1_Cortex_3xTgAD 3xTgAD
|
| 458 |
+
1 G3R3_Cortex_3xTgAD 3xTgAD
|
| 459 |
+
2 G3R4_Cortex_3xTgAD 3xTgAD
|
| 460 |
+
3 G3R10_Cortex_WT WT
|
| 461 |
+
4 G3R7_Cortex_WT WT
|
| 462 |
+
5 G3R9_Cortex_WT WT
|
| 463 |
+
|
| 464 |
+
Preparing PS3O1S DEA genes...
|
| 465 |
+
PS3O1S DEA shape: (48526, 15)
|
| 466 |
+
Columns: ['gene_id', 'gene_name', 'feature', 'fc', 'log2fc', 'pval', 'qval', 'wt.MeanFPKM', 'tg.MeanFPKM', 'FPKM.tau_02', 'FPKM.tau_03', 'FPKM.tau_04', 'FPKM.tau_01', 'FPKM.tau_05', 'FPKM.tau_06']
|
| 467 |
+
Number of genes with pval: 19247
|
| 468 |
+
Top genes:
|
| 469 |
+
gene_id gene_name ... FPKM.tau_05 FPKM.tau_06
|
| 470 |
+
46578 ENSMUSG00000108443 Gm44510 ... 0.859377 1.552261
|
| 471 |
+
47738 ENSMUSG00000109636 RP24-367H14.3 ... 0.025611 0.026643
|
| 472 |
+
13437 ENSMUSG00000045404 Kcnk13 ... 0.000000 0.000000
|
| 473 |
+
15400 ENSMUSG00000052850 Tas2r137 ... 0.064755 0.068036
|
| 474 |
+
5390 ENSMUSG00000026158 Ogfrl1 ... 11.007738 11.835309
|
| 475 |
+
35896 ENSMUSG00000097061 9330151L19Rik ... 5.913222 4.915139
|
| 476 |
+
1520 ENSMUSG00000014748 Tex261 ... 1.444243 1.158760
|
| 477 |
+
9969 ENSMUSG00000035235 Trim13 ... 0.152042 0.140573
|
| 478 |
+
8334 ENSMUSG00000031388 Naa10 ... 3.555390 3.473026
|
| 479 |
+
27321 ENSMUSG00000085382 Gm13861 ... 0.552391 1.398872
|
| 480 |
+
|
| 481 |
+
[10 rows x 15 columns]
|
| 482 |
+
</observation>
|
| 483 |
+
|
| 484 |
+
================================== Ai Message ==================================
|
| 485 |
+
|
| 486 |
+
Good, I have a clear picture of the data now. Let me proceed with running DESeq2 for 5xFAD and 3xTg-AD models.
|
| 487 |
+
|
| 488 |
+
**Plan:**
|
| 489 |
+
1. [✓] Examine the data and prepare count files and metadata for each mouse model
|
| 490 |
+
2. [ ] Run DESeq2 for 5xFAD model (GSE168137)
|
| 491 |
+
3. [ ] Run DESeq2 for 3xTg-AD model (GSE161904)
|
| 492 |
+
4. [ ] Use pre-computed DEA for PS3O1S
|
| 493 |
+
5. [ ] Convert gene IDs to Entrez for KEGG enrichment
|
| 494 |
+
6. [ ] Run KEGG enrichment for all three models
|
| 495 |
+
7. [ ] Combine results into final CSV with shared pathways
|
| 496 |
+
|
| 497 |
+
<execute>
|
| 498 |
+
#!R
|
| 499 |
+
# Run DESeq2 for 5xFAD model
|
| 500 |
+
library(DESeq2)
|
| 501 |
+
|
| 502 |
+
# Read counts
|
| 503 |
+
counts <- as.matrix(read.csv('/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/counts_5xFAD.csv', row.names=1))
|
| 504 |
+
counts <- round(counts)
|
| 505 |
+
|
| 506 |
+
# Read metadata
|
| 507 |
+
metadata <- read.csv('/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/metadata_5xFAD.csv')
|
| 508 |
+
metadata$condition <- factor(metadata$condition, levels=c('WT','5xFAD'))
|
| 509 |
+
|
| 510 |
+
# Clean column names in counts to match metadata
|
| 511 |
+
colnames(counts) <- gsub('^X', '', colnames(counts))
|
| 512 |
+
colnames(counts) <- gsub('\\.', ';', colnames(counts))
|
| 513 |
+
|
| 514 |
+
# Reorder columns to match metadata
|
| 515 |
+
counts <- counts[, metadata$sample]
|
| 516 |
+
|
| 517 |
+
# Create DESeq2 object
|
| 518 |
+
dds <- DESeqDataSetFromMatrix(countData = counts, colData = metadata, design = ~ condition)
|
| 519 |
+
|
| 520 |
+
# Filter low counts
|
| 521 |
+
keep <- rowSums(counts(dds) >= 10) >= 6
|
| 522 |
+
dds <- dds[keep,]
|
| 523 |
+
cat('Genes after filtering:', nrow(dds), '\n')
|
| 524 |
+
|
| 525 |
+
# Run DESeq2
|
| 526 |
+
dds <- DESeq(dds)
|
| 527 |
+
res <- results(dds, contrast=c('condition','5xFAD','WT'))
|
| 528 |
+
res_df <- as.data.frame(res)
|
| 529 |
+
res_df$gene_id <- rownames(res_df)
|
| 530 |
+
write.csv(res_df, 'DEA_5xFAD.csv', row.names=FALSE)
|
| 531 |
+
cat('5xFAD DE genes (padj<0.05):', sum(res$padj < 0.05, na.rm=TRUE), '\n')
|
| 532 |
+
cat('Output written to DEA_5xFAD.csv\n')
|
| 533 |
+
</execute>
|
| 534 |
+
|
| 535 |
+
================================== Ai Message ==================================
|
| 536 |
+
|
| 537 |
+
<observation>Genes after filtering: 16493
|
| 538 |
+
5xFAD DE genes (padj<0.05): 882
|
| 539 |
+
Output written to DEA_5xFAD.csv
|
| 540 |
+
</observation>
|
| 541 |
+
|
| 542 |
+
================================== Ai Message ==================================
|
| 543 |
+
|
| 544 |
+
<execute>
|
| 545 |
+
#!R
|
| 546 |
+
# Run DESeq2 for 3xTg-AD model
|
| 547 |
+
library(DESeq2)
|
| 548 |
+
|
| 549 |
+
# Read counts
|
| 550 |
+
counts <- as.matrix(read.csv('/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/counts_3xTgAD.csv', row.names=1))
|
| 551 |
+
counts <- round(counts)
|
| 552 |
+
|
| 553 |
+
# Read metadata
|
| 554 |
+
metadata <- read.csv('/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/metadata_3xTgAD.csv')
|
| 555 |
+
metadata$condition <- factor(metadata$condition, levels=c('WT','3xTgAD'))
|
| 556 |
+
|
| 557 |
+
# Create DESeq2 object
|
| 558 |
+
dds <- DESeqDataSetFromMatrix(countData = counts, colData = metadata, design = ~ condition)
|
| 559 |
+
|
| 560 |
+
# Filter low counts
|
| 561 |
+
keep <- rowSums(counts(dds) >= 10) >= 3
|
| 562 |
+
dds <- dds[keep,]
|
| 563 |
+
cat('Genes after filtering:', nrow(dds), '\n')
|
| 564 |
+
|
| 565 |
+
# Run DESeq2
|
| 566 |
+
dds <- DESeq(dds)
|
| 567 |
+
res <- results(dds, contrast=c('condition','3xTgAD','WT'))
|
| 568 |
+
res_df <- as.data.frame(res)
|
| 569 |
+
res_df$gene_id <- rownames(res_df)
|
| 570 |
+
write.csv(res_df, 'DEA_3xTgAD.csv', row.names=FALSE)
|
| 571 |
+
cat('3xTg-AD DE genes (padj<0.05):', sum(res$padj < 0.05, na.rm=TRUE), '\n')
|
| 572 |
+
cat('Output written to DEA_3xTgAD.csv\n')
|
| 573 |
+
</execute>
|
| 574 |
+
|
| 575 |
+
================================== Ai Message ==================================
|
| 576 |
+
|
| 577 |
+
<observation>Genes after filtering: 22292
|
| 578 |
+
3xTg-AD DE genes (padj<0.05): 578
|
| 579 |
+
Output written to DEA_3xTgAD.csv
|
| 580 |
+
</observation>
|
| 581 |
+
|
| 582 |
+
================================== Ai Message ==================================
|
| 583 |
+
|
| 584 |
+
Good, both DESeq2 runs completed successfully. Now let me prepare for KEGG enrichment.
|
| 585 |
+
|
| 586 |
+
**Plan:**
|
| 587 |
+
1. [✓] Examine the data and prepare count files and metadata for each mouse model
|
| 588 |
+
2. [✓] Run DESeq2 for 5xFAD model (GSE168137)
|
| 589 |
+
3. [✓] Run DESeq2 for 3xTg-AD model (GSE161904)
|
| 590 |
+
4. [ ] Use pre-computed DEA for PS3O1S
|
| 591 |
+
5. [ ] Convert gene IDs to Entrez for KEGG enrichment
|
| 592 |
+
6. [ ] Run KEGG enrichment for all three models
|
| 593 |
+
7. [ ] Combine results into final CSV with shared pathways
|
| 594 |
+
|
| 595 |
+
<execute>
|
| 596 |
+
#!R
|
| 597 |
+
# Examine DEA results and prepare gene lists for KEGG enrichment
|
| 598 |
+
cat("=== Checking DEA 5xFAD ===\n")
|
| 599 |
+
de5 <- read.csv('/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/DEA_5xFAD.csv')
|
| 600 |
+
cat('5xFAD columns:', colnames(de5), '\n')
|
| 601 |
+
cat('5xFAD total rows:', nrow(de5), '\n')
|
| 602 |
+
cat('5xFAD DE genes (padj<0.05):', sum(de5$padj < 0.05, na.rm=TRUE), '\n')
|
| 603 |
+
|
| 604 |
+
cat("\n=== Checking DEA 3xTgAD ===\n")
|
| 605 |
+
de3 <- read.csv('/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/DEA_3xTgAD.csv')
|
| 606 |
+
cat('3xTgAD columns:', colnames(de3), '\n')
|
| 607 |
+
cat('3xTgAD total rows:', nrow(de3), '\n')
|
| 608 |
+
cat('3xTgAD DE genes (padj<0.05):', sum(de3$padj < 0.05, na.rm=TRUE), '\n')
|
| 609 |
+
|
| 610 |
+
cat("\n=== Checking PS3O1S ===\n")
|
| 611 |
+
ps3 <- read.csv('/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/DEA_PS3O1S.csv')
|
| 612 |
+
cat('PS3O1S columns:', colnames(ps3), '\n')
|
| 613 |
+
cat('PS3O1S total rows:', nrow(ps3), '\n')
|
| 614 |
+
cat('PS3O1S genes with pval:', sum(!is.na(ps3$pval)), '\n')
|
| 615 |
+
cat('PS3O1S significant (pval<0.05):', sum(ps3$pval < 0.05, na.rm=TRUE), '\n')
|
| 616 |
+
</execute>
|
| 617 |
+
|
| 618 |
+
================================== Ai Message ==================================
|
| 619 |
+
|
| 620 |
+
<observation>Error running R code:
|
| 621 |
+
Error in file(file, "rt") : cannot open the connection
|
| 622 |
+
Calls: read.csv -> read.table -> file
|
| 623 |
+
In addition: Warning message:
|
| 624 |
+
In file(file, "rt") :
|
| 625 |
+
cannot open file '/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/DEA_5xFAD.csv': No such file or directory
|
| 626 |
+
Execution halted
|
| 627 |
+
</observation>
|
| 628 |
+
|
| 629 |
+
================================== Ai Message ==================================
|
| 630 |
+
|
| 631 |
+
<execute>
|
| 632 |
+
#!BASH
|
| 633 |
+
echo "Checking directory and files..."
|
| 634 |
+
ls -la /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/
|
| 635 |
+
echo ""
|
| 636 |
+
echo "Checking with alternative path..."
|
| 637 |
+
ls -la /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/DEA_*
|
| 638 |
+
</execute>
|
| 639 |
+
|
| 640 |
+
================================== Ai Message ==================================
|
| 641 |
+
|
| 642 |
+
<observation>Error running Bash script (exit code 2):
|
| 643 |
+
ls: cannot access '/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/DEA_*': No such file or directory
|
| 644 |
+
</observation>
|
| 645 |
+
|
| 646 |
+
================================== Ai Message ==================================
|
| 647 |
+
|
| 648 |
+
<execute>
|
| 649 |
+
#!BASH
|
| 650 |
+
echo "Current working directory:"
|
| 651 |
+
pwd
|
| 652 |
+
echo ""
|
| 653 |
+
echo "Checking the run directory path:"
|
| 654 |
+
ls -la /225040511/project/
|
| 655 |
+
echo ""
|
| 656 |
+
echo "Looking for the exact run directory:"
|
| 657 |
+
find /225040511/project/ -name "*alzheimer-mouse*" -type d 2>/dev/null
|
| 658 |
+
</execute>
|
| 659 |
+
|
| 660 |
+
================================== Ai Message ==================================
|
| 661 |
+
|
| 662 |
+
<observation>Current working directory:
|
| 663 |
+
/225040511/project/Biomni/experiments/bioagent_bench/scripts
|
| 664 |
+
|
| 665 |
+
Checking the run directory path:
|
| 666 |
+
total 4193616
|
| 667 |
+
drwxr-xr-x 30 root root 4096 May 14 10:47 .
|
| 668 |
+
drwx------ 22 86443 root 4096 May 14 19:25 ..
|
| 669 |
+
drwxr-xr-x 15 root root 4096 May 5 04:40 BioScientist
|
| 670 |
+
drwxr-xr-x 6 root root 4096 Apr 20 11:36 BioinfoMCP-main
|
| 671 |
+
drwxr-xr-x 10 root root 4096 May 14 11:19 Biomni
|
| 672 |
+
drwxr-xr-x 2 root root 4096 Mar 5 05:36 Dermnet_index
|
| 673 |
+
drwxr-xr-x 7 root root 4096 Apr 29 04:54 EHRFormer
|
| 674 |
+
drwxr-xr-x 4 root root 4096 Feb 18 09:01 Evaluation_Logs
|
| 675 |
+
drwxr-xr-x 19 root root 4096 Apr 24 10:30 Evaluation_Results
|
| 676 |
+
drwxr-xr-x 3 root root 4096 Dec 17 08:55 Hulumed_reasoning_results
|
| 677 |
+
drwxr-xr-x 4 root root 4096 Dec 2 07:58 Hulumed_scripts
|
| 678 |
+
drwxr-xr-x 17 root root 4096 May 14 18:07 Hypo_Bio_OS
|
| 679 |
+
drwxr-xr-x 16 root root 4096 May 13 13:04 LAB-Bench
|
| 680 |
+
drwxr-xr-x 7 root root 4096 Dec 22 08:18 PanDerm
|
| 681 |
+
drwxr-xr-x 4 root root 4096 Dec 22 14:47 Panderm-EvaluationResults
|
| 682 |
+
drwxr-xr-x 4 root root 4096 Dec 19 12:53 SkinGPT-X-EvaluationResults
|
| 683 |
+
drwxr-xr-x 9 root root 4096 Apr 7 13:53 Skingpt_X
|
| 684 |
+
drwxr-xr-x 10 root root 4096 Apr 7 13:42 Skingpt_X_save
|
| 685 |
+
drwxr-xr-x 8 root root 4096 May 7 06:10 autodiscovery
|
| 686 |
+
drwxr-xr-x 7 root root 4096 May 13 06:41 bioagent-bench
|
| 687 |
+
drwxr-xr-x 13 root root 4096 Dec 21 13:28 graphrag
|
| 688 |
+
drwxr-xr-x 21 root root 4096 Apr 23 11:23 hf_cache
|
| 689 |
+
drwxr-xr-x 3 root root 4096 Jan 13 13:39 medgamma_reasoning_results
|
| 690 |
+
drwxr-xr-x 3 root root 4096 Jan 21 07:18 medgamma_scripts
|
| 691 |
+
drwxr-xr-x 7 root root 4096 Dec 28 09:41 my_graph
|
| 692 |
+
drwxr-xr-x 5 root root 4096 Mar 7 09:17 new_dataset
|
| 693 |
+
drwxr-xr-x 3 root root 4096 Mar 10 05:51 ollama
|
| 694 |
+
-rw-r--r-- 1 root root 4294242395 Dec 20 15:16 ollama-models.tar.gz
|
| 695 |
+
-rw-r--r-- 1 root root 2598 Dec 21 13:03 ollama.log
|
| 696 |
+
drwxr-xr-x 8 root root 4096 May 12 07:55 promptbench
|
| 697 |
+
drwxr-xr-x 15 root root 4096 May 11 12:03 strata_bio_platform
|
| 698 |
+
drwxr-xr-x 9 root root 4096 Jan 24 09:07 user_dwf
|
| 699 |
+
|
| 700 |
+
Looking for the exact run directory:
|
| 701 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_500/alzheimer-mouse_20260515_092052
|
| 702 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_500/alzheimer-mouse_20260515_092207
|
| 703 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_500/alzheimer-mouse_20260515_093531
|
| 704 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_100/alzheimer-mouse_20260514_163442
|
| 705 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_133826
|
| 706 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905
|
| 707 |
+
/225040511/project/Hypo_Bio_OS/bioagent-bench-runs/alzheimer-mouse_20260513_101914
|
| 708 |
+
/225040511/project/Hypo_Bio_OS/bioagent-bench-runs/alzheimer-mouse_20260514_055459
|
| 709 |
+
/225040511/project/bioagent-bench/dataset/alzheimer-mouse
|
| 710 |
+
</observation>
|
| 711 |
+
|
| 712 |
+
================================== Ai Message ==================================
|
| 713 |
+
|
| 714 |
+
<execute>
|
| 715 |
+
#!BASH
|
| 716 |
+
echo "Checking current directory for output files..."
|
| 717 |
+
ls -la /225040511/project/Biomni/experiments/bioagent_bench/scripts/
|
| 718 |
+
echo ""
|
| 719 |
+
echo "Checking alternative paths:"
|
| 720 |
+
find /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/ -type f 2>/dev/null
|
| 721 |
+
</execute>
|
| 722 |
+
|
| 723 |
+
================================== Ai Message ==================================
|
| 724 |
+
|
| 725 |
+
<observation>Checking current directory for output files...
|
| 726 |
+
total 5250
|
| 727 |
+
drwxr-xr-x 3 root root 4096 May 15 13:52 .
|
| 728 |
+
drwxr-xr-x 6 root root 4096 May 15 06:35 ..
|
| 729 |
+
-rw-r--r-- 1 root root 2875989 May 15 13:52 DEA_3xTgAD.csv
|
| 730 |
+
-rw-r--r-- 1 root root 2131277 May 15 13:51 DEA_5xFAD.csv
|
| 731 |
+
drwxr-xr-x 2 root root 4096 May 15 07:01 __pycache__
|
| 732 |
+
-rwxr-xr-x 1 root root 21551 May 14 16:31 evaluate_mcp_scaling_runs.py
|
| 733 |
+
-rw-r--r-- 1 root root 9788 May 14 05:40 generate_mcp_scale_configs.py
|
| 734 |
+
-rwxr-xr-x 1 root root 21403 May 15 06:56 run_bioagent_bench_with_biomni.py
|
| 735 |
+
-rwxr-xr-x 1 root root 4478 May 15 07:19 run_biomni_scaling_experiment.sh
|
| 736 |
+
-rw-r--r-- 1 root root 8173 May 15 07:00 summarize_biomni_task_metrics.py
|
| 737 |
+
-rw-r--r-- 1 root root 3254 May 14 16:31 summarize_scaling_table.py
|
| 738 |
+
|
| 739 |
+
Checking alternative paths:
|
| 740 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/counts_3xTgAD.csv
|
| 741 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/task_query.txt
|
| 742 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/metadata_3xTgAD.csv
|
| 743 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/counts_5xFAD.csv
|
| 744 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/run_metadata.json
|
| 745 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/metadata_5xFAD.csv
|
| 746 |
+
</observation>
|
| 747 |
+
|
| 748 |
+
================================== Ai Message ==================================
|
| 749 |
+
|
| 750 |
+
I see the R scripts wrote outputs to the current working directory (scripts) instead of the run directory. Let me fix this.
|
| 751 |
+
|
| 752 |
+
<execute>
|
| 753 |
+
#!BASH
|
| 754 |
+
echo "Copying DEA results to run directory..."
|
| 755 |
+
cp /225040511/project/Biomni/experiments/bioagent_bench/scripts/DEA_5xFAD.csv /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/
|
| 756 |
+
cp /225040511/project/Biomni/experiments/bioagent_bench/scripts/DEA_3xTgAD.csv /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/
|
| 757 |
+
echo "Done copying"
|
| 758 |
+
ls -la /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/
|
| 759 |
+
</execute>
|
| 760 |
+
|
| 761 |
+
================================== Ai Message ==================================
|
| 762 |
+
|
| 763 |
+
<observation>Copying DEA results to run directory...
|
| 764 |
+
Done copying
|
| 765 |
+
total 7747
|
| 766 |
+
drwxr-xr-x 3 root root 4096 May 15 13:52 .
|
| 767 |
+
drwxr-xr-x 4 root root 4096 May 15 13:49 ..
|
| 768 |
+
-rw-r--r-- 1 root root 2875989 May 15 13:52 DEA_3xTgAD.csv
|
| 769 |
+
-rw-r--r-- 1 root root 2131277 May 15 13:52 DEA_5xFAD.csv
|
| 770 |
+
drwxr-xr-x 3 root root 4096 May 15 13:49 agent_runtime
|
| 771 |
+
-rw-r--r-- 1 root root 1622892 May 15 13:50 counts_3xTgAD.csv
|
| 772 |
+
-rw-r--r-- 1 root root 6204071 May 15 13:50 counts_5xFAD.csv
|
| 773 |
+
-rw-r--r-- 1 root root 150 May 15 13:50 metadata_3xTgAD.csv
|
| 774 |
+
-rw-r--r-- 1 root root 687 May 15 13:50 metadata_5xFAD.csv
|
| 775 |
+
-rw-r--r-- 1 root root 4390 May 15 13:49 run_metadata.json
|
| 776 |
+
-rw-r--r-- 1 root root 2702 May 15 13:49 task_query.txt
|
| 777 |
+
</observation>
|
| 778 |
+
|
| 779 |
+
================================== Ai Message ==================================
|
| 780 |
+
|
| 781 |
+
Now let me examine the DEA results and prepare for KEGG enrichment.
|
| 782 |
+
|
| 783 |
+
<execute>
|
| 784 |
+
#!R
|
| 785 |
+
# Examine DEA results
|
| 786 |
+
cat("=== DEA 5xFAD first few rows ===\n")
|
| 787 |
+
de5 <- read.csv('/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/DEA_5xFAD.csv')
|
| 788 |
+
cat('Columns:', colnames(de5), '\n')
|
| 789 |
+
cat('Rows:', nrow(de5), '\n')
|
| 790 |
+
cat('Genes with padj < 0.05:', sum(de5$padj < 0.05, na.rm=TRUE), '\n')
|
| 791 |
+
cat('First 3 genes:\n')
|
| 792 |
+
print(head(de5[,c('gene_id','log2FoldChange','padj')], 3))
|
| 793 |
+
|
| 794 |
+
cat('\n=== DEA 3xTgAD first few rows ===\n')
|
| 795 |
+
de3 <- read.csv('/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/DEA_3xTgAD.csv')
|
| 796 |
+
cat('Columns:', colnames(de3), '\n')
|
| 797 |
+
cat('Rows:', nrow(de3), '\n')
|
| 798 |
+
cat('Genes with padj < 0.05:', sum(de3$padj < 0.05, na.rm=TRUE), '\n')
|
| 799 |
+
cat('First 3 genes:\n')
|
| 800 |
+
print(head(de3[,c('gene_id','log2FoldChange','padj')], 3))
|
| 801 |
+
|
| 802 |
+
cat('\n=== PS3O1S first few rows ===\n')
|
| 803 |
+
ps3 <- read.csv('/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/DEA_PS3O1S.csv')
|
| 804 |
+
cat('Columns:', colnames(ps3), '\n')
|
| 805 |
+
cat('Rows:', nrow(ps3), '\n')
|
| 806 |
+
cat('Genes with pval < 0.05 (non-NA):', sum(ps3$pval < 0.05, na.rm=TRUE), '\n')
|
| 807 |
+
cat('First 3 genes:\n')
|
| 808 |
+
print(head(ps3[,c('gene_id','gene_name','log2fc','pval')], 3))
|
| 809 |
+
</execute>
|
| 810 |
+
|
| 811 |
+
================================== Ai Message ==================================
|
| 812 |
+
|
| 813 |
+
<observation>=== DEA 5xFAD first few rows ===
|
| 814 |
+
Columns: baseMean log2FoldChange lfcSE stat pvalue padj gene_id
|
| 815 |
+
Rows: 16493
|
| 816 |
+
Genes with padj < 0.05: 882
|
| 817 |
+
First 3 genes:
|
| 818 |
+
gene_id log2FoldChange padj
|
| 819 |
+
1 ENSMUSG00000000001 -0.01507036 0.9980869
|
| 820 |
+
2 ENSMUSG00000000028 0.04354083 0.9980869
|
| 821 |
+
3 ENSMUSG00000000049 0.08951066 0.9980869
|
| 822 |
+
|
| 823 |
+
=== DEA 3xTgAD first few rows ===
|
| 824 |
+
Columns: baseMean log2FoldChange lfcSE stat pvalue padj gene_id
|
| 825 |
+
Rows: 22292
|
| 826 |
+
Genes with padj < 0.05: 578
|
| 827 |
+
First 3 genes:
|
| 828 |
+
gene_id log2FoldChange padj
|
| 829 |
+
1 ENSMUSG00000000001 0.04920982 0.9999671
|
| 830 |
+
2 ENSMUSG00000000028 -0.25938298 0.9999671
|
| 831 |
+
3 ENSMUSG00000000037 -0.23516499 0.9999671
|
| 832 |
+
|
| 833 |
+
=== PS3O1S first few rows ===
|
| 834 |
+
Columns: X gene_id gene_name feature fc log2fc pval qval wt.MeanFPKM tg.MeanFPKM FPKM.tau_02 FPKM.tau_03 FPKM.tau_04 FPKM.tau_01 FPKM.tau_05 FPKM.tau_06
|
| 835 |
+
Rows: 48526
|
| 836 |
+
Genes with pval < 0.05 (non-NA): 797
|
| 837 |
+
First 3 genes:
|
| 838 |
+
gene_id gene_name log2fc pval
|
| 839 |
+
1 ENSMUSG00000000001 Gnai3 0.09420766 0.6001159
|
| 840 |
+
2 ENSMUSG00000000003 Pbsn 0.00000000 NA
|
| 841 |
+
3 ENSMUSG00000000028 Cdc45 0.00000000 NA
|
| 842 |
+
</observation>
|
| 843 |
+
|
| 844 |
+
================================== Ai Message ==================================
|
| 845 |
+
|
| 846 |
+
Good, I have the DEA results. Now let me get the Entrez IDs and run KEGG enrichment.
|
| 847 |
+
|
| 848 |
+
<execute>
|
| 849 |
+
#!R
|
| 850 |
+
# Check PS3O1S qval information
|
| 851 |
+
ps3 <- read.csv('/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/DEA_PS3O1S.csv')
|
| 852 |
+
cat('PS3O1S significant genes with pval<0.05:', sum(ps3$pval < 0.05, na.rm=TRUE), '\n')
|
| 853 |
+
cat('PS3O1S significant genes with qval<0.05:', sum(ps3$qval < 0.05, na.rm=TRUE), '\n')
|
| 854 |
+
cat('Non-NA pval count:', sum(!is.na(ps3$pval)), '\n')
|
| 855 |
+
cat('Non-NA qval count:', sum(!is.na(ps3$qval)), '\n')
|
| 856 |
+
</execute>
|
| 857 |
+
|
| 858 |
+
================================== Ai Message ==================================
|
| 859 |
+
|
| 860 |
+
<observation>PS3O1S significant genes with pval<0.05: 797
|
| 861 |
+
PS3O1S significant genes with qval<0.05: 1
|
| 862 |
+
Non-NA pval count: 19247
|
| 863 |
+
Non-NA qval count: 19247
|
| 864 |
+
</observation>
|
| 865 |
+
|
| 866 |
+
================================== Ai Message ==================================
|
| 867 |
+
|
| 868 |
+
Now let me run KEGG enrichment for all three models.
|
| 869 |
+
|
| 870 |
+
**Plan:**
|
| 871 |
+
1. [✓] Examine the data and prepare count files and metadata for each mouse model
|
| 872 |
+
2. [✓] Run DESeq2 for 5xFAD model (GSE168137)
|
| 873 |
+
3. [✓] Run DESeq2 for 3xTg-AD model (GSE161904)
|
| 874 |
+
4. [✓] Use pre-computed DEA for PS3O1S
|
| 875 |
+
5. [ ] Convert gene IDs to Entrez for KEGG enrichment
|
| 876 |
+
6. [ ] Run KEGG enrichment for all three models
|
| 877 |
+
7. [ ] Combine results into final CSV with shared pathways
|
| 878 |
+
|
| 879 |
+
<execute>
|
| 880 |
+
#!R
|
| 881 |
+
# Get Entrez IDs for all genes using org.Mm.eg.db
|
| 882 |
+
library(org.Mm.eg.db)
|
| 883 |
+
|
| 884 |
+
# Read DEA files
|
| 885 |
+
de5 <- read.csv('/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/DEA_5xFAD.csv')
|
| 886 |
+
de3 <- read.csv('/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/DEA_3xTgAD.csv')
|
| 887 |
+
ps3 <- read.csv('/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data/DEA_PS3O1S.csv')
|
| 888 |
+
|
| 889 |
+
# Get significant genes for each model (using pval < 0.05 for all to be consistent)
|
| 890 |
+
sig5 <- de5$gene_id[which(de5$padj < 0.05)]
|
| 891 |
+
sig3 <- de3$gene_id[which(de3$padj < 0.05)]
|
| 892 |
+
sig_ps3 <- ps3$gene_id[which(ps3$pval < 0.05)]
|
| 893 |
+
|
| 894 |
+
cat('5xFAD significant genes:', length(sig5), '\n')
|
| 895 |
+
cat('3xTgAD significant genes:', length(sig3), '\n')
|
| 896 |
+
cat('PS3O1S significant genes:', length(sig_ps3), '\n')
|
| 897 |
+
|
| 898 |
+
# Map Ensembl IDs to Entrez IDs for each set
|
| 899 |
+
entrez5 <- mapIds(org.Mm.eg.db, keys=sig5, keytype='ENSEMBL', column='ENTREZID')
|
| 900 |
+
entrez3 <- mapIds(org.Mm.eg.db, keys=sig3, keytype='ENSEMBL', column='ENTREZID')
|
| 901 |
+
entrez_ps3 <- mapIds(org.Mm.eg.db, keys=sig_ps3, keytype='ENSEMBL', column='ENTREZID')
|
| 902 |
+
|
| 903 |
+
# Remove NAs
|
| 904 |
+
entrez5 <- entrez5[!is.na(entrez5)]
|
| 905 |
+
entrez3 <- entrez3[!is.na(entrez3)]
|
| 906 |
+
entrez_ps3 <- entrez_ps3[!is.na(entrez_ps3)]
|
| 907 |
+
|
| 908 |
+
cat('5xFAD with Entrez IDs:', length(entrez5), '\n')
|
| 909 |
+
cat('3xTgAD with Entrez IDs:', length(entrez3), '\n')
|
| 910 |
+
cat('PS3O1S with Entrez IDs:', length(entrez_ps3), '\n')
|
| 911 |
+
|
| 912 |
+
# Save Entrez IDs for later use
|
| 913 |
+
write(as.character(entrez5), 'entrez_5xFAD.txt')
|
| 914 |
+
write(as.character(entrez3), 'entrez_3xTgAD.txt')
|
| 915 |
+
write(as.character(entrez_ps3), 'entrez_PS3O1S.txt')
|
| 916 |
+
cat('Entrez lists saved.\n')
|
| 917 |
+
</execute>
|
| 918 |
+
|
| 919 |
+
================================== Ai Message ==================================
|
| 920 |
+
|
| 921 |
+
<observation>5xFAD significant genes: 882
|
| 922 |
+
3xTgAD significant genes: 578
|
| 923 |
+
PS3O1S significant genes: 797
|
| 924 |
+
5xFAD with Entrez IDs: 873
|
| 925 |
+
3xTgAD with Entrez IDs: 485
|
| 926 |
+
PS3O1S with Entrez IDs: 633
|
| 927 |
+
Entrez lists saved.
|
| 928 |
+
</observation>
|
| 929 |
+
|
| 930 |
+
================================== Ai Message ==================================
|
| 931 |
+
|
| 932 |
+
Now let me run KEGG enrichment for all three models.
|
| 933 |
+
|
| 934 |
+
<execute>
|
| 935 |
+
#!R
|
| 936 |
+
# Run KEGG enrichment using clusterProfiler
|
| 937 |
+
library(clusterProfiler)
|
| 938 |
+
library(org.Mm.eg.db)
|
| 939 |
+
|
| 940 |
+
# Set working directory to the run directory
|
| 941 |
+
setwd('/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905')
|
| 942 |
+
|
| 943 |
+
# Read Entrez IDs
|
| 944 |
+
entrez5 <- readLines('entrez_5xFAD.txt')
|
| 945 |
+
entrez3 <- readLines('entrez_3xTgAD.txt')
|
| 946 |
+
entrez_ps3 <- readLines('entrez_PS3O1S.txt')
|
| 947 |
+
|
| 948 |
+
cat('5xFAD entrez count:', length(entrez5), '\n')
|
| 949 |
+
cat('3xTgAD entrez count:', length(entrez3), '\n')
|
| 950 |
+
cat('PS3O1S entrez count:', length(entrez_ps3), '\n')
|
| 951 |
+
|
| 952 |
+
# Run KEGG enrichment for 5xFAD
|
| 953 |
+
cat('\n=== Running KEGG enrichment for 5xFAD ===\n')
|
| 954 |
+
kegg5 <- enrichKEGG(gene = entrez5, organism = 'mmu', pvalueCutoff = 0.05, qvalueCutoff = 0.2)
|
| 955 |
+
if (!is.null(kegg5)) {
|
| 956 |
+
write.csv(as.data.frame(kegg5), 'kegg_5xFAD.csv', row.names=FALSE)
|
| 957 |
+
cat('KEGG 5xFAD enriched pathways:', nrow(kegg5), '\n')
|
| 958 |
+
} else {
|
| 959 |
+
cat('No KEGG enrichment results for 5xFAD\n')
|
| 960 |
+
}
|
| 961 |
+
|
| 962 |
+
# Run KEGG enrichment for 3xTgAD
|
| 963 |
+
cat('\n=== Running KEGG enrichment for 3xTgAD ===\n')
|
| 964 |
+
kegg3 <- enrichKEGG(gene = entrez3, organism = 'mmu', pvalueCutoff = 0.05, qvalueCutoff = 0.2)
|
| 965 |
+
if (!is.null(kegg3)) {
|
| 966 |
+
write.csv(as.data.frame(kegg3), 'kegg_3xTgAD.csv', row.names=FALSE)
|
| 967 |
+
cat('KEGG 3xTgAD enriched pathways:', nrow(kegg3), '\n')
|
| 968 |
+
} else {
|
| 969 |
+
cat('No KEGG enrichment results for 3xTgAD\n')
|
| 970 |
+
}
|
| 971 |
+
|
| 972 |
+
# Run KEGG enrichment for PS3O1S
|
| 973 |
+
cat('\n=== Running KEGG enrichment for PS3O1S ===\n')
|
| 974 |
+
kegg_ps3 <- enrichKEGG(gene = entrez_ps3, organism = 'mmu', pvalueCutoff = 0.05, qvalueCutoff = 0.2)
|
| 975 |
+
if (!is.null(kegg_ps3)) {
|
| 976 |
+
write.csv(as.data.frame(kegg_ps3), 'kegg_PS3O1S.csv', row.names=FALSE)
|
| 977 |
+
cat('KEGG PS3O1S enriched pathways:', nrow(kegg_ps3), '\n')
|
| 978 |
+
} else {
|
| 979 |
+
cat('No KEGG enrichment results for PS3O1S\n')
|
| 980 |
+
}
|
| 981 |
+
|
| 982 |
+
# List files created
|
| 983 |
+
cat('\n=== Files created in run directory ===\n')
|
| 984 |
+
list.files(pattern='kegg_')
|
| 985 |
+
</execute>
|
| 986 |
+
|
| 987 |
+
================================== Ai Message ==================================
|
| 988 |
+
|
| 989 |
+
<observation>Error running R code:
|
| 990 |
+
Error in library(clusterProfiler) :
|
| 991 |
+
there is no package called ‘clusterProfiler’
|
| 992 |
+
Execution halted
|
| 993 |
+
</observation>
|
| 994 |
+
|
| 995 |
+
================================== Ai Message ==================================
|
| 996 |
+
|
| 997 |
+
<execute>
|
| 998 |
+
#!R
|
| 999 |
+
# Check available packages
|
| 1000 |
+
cat("Installed packages:\n")
|
| 1001 |
+
ip <- installed.packages()
|
| 1002 |
+
cat(ip[,1], sep='\n')
|
| 1003 |
+
cat('\n\nSearching for clusterProfiler or similar...\n')
|
| 1004 |
+
cat(grep('clusterProfiler|enrich|KEGG', ip[,1], value=TRUE, ignore.case=TRUE), sep='\n')
|
| 1005 |
+
</execute>
|
| 1006 |
+
|
| 1007 |
+
================================== Ai Message ==================================
|
| 1008 |
+
|
| 1009 |
+
<observation>Installed packages:
|
| 1010 |
+
abind
|
| 1011 |
+
AnnotationDbi
|
| 1012 |
+
ape
|
| 1013 |
+
aplot
|
| 1014 |
+
argparse
|
| 1015 |
+
askpass
|
| 1016 |
+
assertthat
|
| 1017 |
+
backports
|
| 1018 |
+
base
|
| 1019 |
+
base64enc
|
| 1020 |
+
BH
|
| 1021 |
+
Biobase
|
| 1022 |
+
BiocGenerics
|
| 1023 |
+
BiocManager
|
| 1024 |
+
BiocParallel
|
| 1025 |
+
BiocVersion
|
| 1026 |
+
Biostrings
|
| 1027 |
+
bit
|
| 1028 |
+
bit64
|
| 1029 |
+
blob
|
| 1030 |
+
boot
|
| 1031 |
+
broom
|
| 1032 |
+
bslib
|
| 1033 |
+
cachem
|
| 1034 |
+
callr
|
| 1035 |
+
caret
|
| 1036 |
+
cellranger
|
| 1037 |
+
class
|
| 1038 |
+
cli
|
| 1039 |
+
clipr
|
| 1040 |
+
clock
|
| 1041 |
+
cluster
|
| 1042 |
+
codetools
|
| 1043 |
+
colorspace
|
| 1044 |
+
commonmark
|
| 1045 |
+
compiler
|
| 1046 |
+
conflicted
|
| 1047 |
+
cowplot
|
| 1048 |
+
cpp11
|
| 1049 |
+
crayon
|
| 1050 |
+
crul
|
| 1051 |
+
curl
|
| 1052 |
+
data.table
|
| 1053 |
+
datasets
|
| 1054 |
+
DBI
|
| 1055 |
+
dbplyr
|
| 1056 |
+
DelayedArray
|
| 1057 |
+
DESeq2
|
| 1058 |
+
diagram
|
| 1059 |
+
digest
|
| 1060 |
+
DOSE
|
| 1061 |
+
dplyr
|
| 1062 |
+
dtplyr
|
| 1063 |
+
e1071
|
| 1064 |
+
ellipsis
|
| 1065 |
+
evaluate
|
| 1066 |
+
fansi
|
| 1067 |
+
farver
|
| 1068 |
+
fastmap
|
| 1069 |
+
fastmatch
|
| 1070 |
+
fgsea
|
| 1071 |
+
findpython
|
| 1072 |
+
fontawesome
|
| 1073 |
+
fontBitstreamVera
|
| 1074 |
+
fontLiberation
|
| 1075 |
+
fontquiver
|
| 1076 |
+
forcats
|
| 1077 |
+
foreach
|
| 1078 |
+
foreign
|
| 1079 |
+
formatR
|
| 1080 |
+
fs
|
| 1081 |
+
futile.logger
|
| 1082 |
+
futile.options
|
| 1083 |
+
future
|
| 1084 |
+
future.apply
|
| 1085 |
+
gargle
|
| 1086 |
+
generics
|
| 1087 |
+
GenomeInfoDb
|
| 1088 |
+
GenomicRanges
|
| 1089 |
+
ggforce
|
| 1090 |
+
ggfun
|
| 1091 |
+
ggnewscale
|
| 1092 |
+
ggplot2
|
| 1093 |
+
ggplotify
|
| 1094 |
+
ggrepel
|
| 1095 |
+
ggtangle
|
| 1096 |
+
gistr
|
| 1097 |
+
glmnet
|
| 1098 |
+
globals
|
| 1099 |
+
glue
|
| 1100 |
+
GO.db
|
| 1101 |
+
googledrive
|
| 1102 |
+
googlesheets4
|
| 1103 |
+
GOSemSim
|
| 1104 |
+
gower
|
| 1105 |
+
graphics
|
| 1106 |
+
grDevices
|
| 1107 |
+
grid
|
| 1108 |
+
gridGraphics
|
| 1109 |
+
gson
|
| 1110 |
+
gtable
|
| 1111 |
+
gtools
|
| 1112 |
+
hardhat
|
| 1113 |
+
haven
|
| 1114 |
+
hexbin
|
| 1115 |
+
highr
|
| 1116 |
+
hms
|
| 1117 |
+
htmltools
|
| 1118 |
+
htmlwidgets
|
| 1119 |
+
httpcode
|
| 1120 |
+
httpuv
|
| 1121 |
+
httr
|
| 1122 |
+
ids
|
| 1123 |
+
igraph
|
| 1124 |
+
ipred
|
| 1125 |
+
IRanges
|
| 1126 |
+
IRdisplay
|
| 1127 |
+
IRkernel
|
| 1128 |
+
isoband
|
| 1129 |
+
iterators
|
| 1130 |
+
jquerylib
|
| 1131 |
+
jsonlite
|
| 1132 |
+
KEGGREST
|
| 1133 |
+
KernSmooth
|
| 1134 |
+
knitr
|
| 1135 |
+
labeling
|
| 1136 |
+
lambda.r
|
| 1137 |
+
later
|
| 1138 |
+
lattice
|
| 1139 |
+
lava
|
| 1140 |
+
lazyeval
|
| 1141 |
+
lifecycle
|
| 1142 |
+
listenv
|
| 1143 |
+
lobstr
|
| 1144 |
+
locfit
|
| 1145 |
+
lubridate
|
| 1146 |
+
magrittr
|
| 1147 |
+
maps
|
| 1148 |
+
MASS
|
| 1149 |
+
Matrix
|
| 1150 |
+
MatrixGenerics
|
| 1151 |
+
matrixStats
|
| 1152 |
+
memoise
|
| 1153 |
+
methods
|
| 1154 |
+
mgcv
|
| 1155 |
+
mime
|
| 1156 |
+
ModelMetrics
|
| 1157 |
+
modelr
|
| 1158 |
+
munsell
|
| 1159 |
+
nlme
|
| 1160 |
+
nnet
|
| 1161 |
+
numDeriv
|
| 1162 |
+
openssl
|
| 1163 |
+
org.Hs.eg.db
|
| 1164 |
+
org.Mm.eg.db
|
| 1165 |
+
otel
|
| 1166 |
+
parallel
|
| 1167 |
+
parallelly
|
| 1168 |
+
patchwork
|
| 1169 |
+
pbdZMQ
|
| 1170 |
+
pillar
|
| 1171 |
+
pkgconfig
|
| 1172 |
+
plyr
|
| 1173 |
+
png
|
| 1174 |
+
polyclip
|
| 1175 |
+
prettyunits
|
| 1176 |
+
pROC
|
| 1177 |
+
processx
|
| 1178 |
+
prodlim
|
| 1179 |
+
progress
|
| 1180 |
+
progressr
|
| 1181 |
+
promises
|
| 1182 |
+
proxy
|
| 1183 |
+
pryr
|
| 1184 |
+
ps
|
| 1185 |
+
purrr
|
| 1186 |
+
quantmod
|
| 1187 |
+
qvalue
|
| 1188 |
+
R.methodsS3
|
| 1189 |
+
R.oo
|
| 1190 |
+
R.utils
|
| 1191 |
+
R6
|
| 1192 |
+
ragg
|
| 1193 |
+
randomForest
|
| 1194 |
+
rappdirs
|
| 1195 |
+
rbokeh
|
| 1196 |
+
RColorBrewer
|
| 1197 |
+
Rcpp
|
| 1198 |
+
RcppArmadillo
|
| 1199 |
+
RcppEigen
|
| 1200 |
+
readr
|
| 1201 |
+
readxl
|
| 1202 |
+
recipes
|
| 1203 |
+
rematch
|
| 1204 |
+
rematch2
|
| 1205 |
+
repr
|
| 1206 |
+
reprex
|
| 1207 |
+
reshape2
|
| 1208 |
+
rlang
|
| 1209 |
+
rmarkdown
|
| 1210 |
+
rpart
|
| 1211 |
+
RSQLite
|
| 1212 |
+
rstudioapi
|
| 1213 |
+
rvest
|
| 1214 |
+
S4Arrays
|
| 1215 |
+
S4Vectors
|
| 1216 |
+
S7
|
| 1217 |
+
sass
|
| 1218 |
+
scales
|
| 1219 |
+
scatterpie
|
| 1220 |
+
selectr
|
| 1221 |
+
Seqinfo
|
| 1222 |
+
shape
|
| 1223 |
+
shiny
|
| 1224 |
+
snow
|
| 1225 |
+
sourcetools
|
| 1226 |
+
SparseArray
|
| 1227 |
+
sparsevctrs
|
| 1228 |
+
spatial
|
| 1229 |
+
splines
|
| 1230 |
+
SQUAREM
|
| 1231 |
+
statmod
|
| 1232 |
+
stats
|
| 1233 |
+
stats4
|
| 1234 |
+
stringi
|
| 1235 |
+
stringr
|
| 1236 |
+
SummarizedExperiment
|
| 1237 |
+
survival
|
| 1238 |
+
sys
|
| 1239 |
+
systemfonts
|
| 1240 |
+
tcltk
|
| 1241 |
+
textshaping
|
| 1242 |
+
tibble
|
| 1243 |
+
tidydr
|
| 1244 |
+
tidyr
|
| 1245 |
+
tidyselect
|
| 1246 |
+
tidytree
|
| 1247 |
+
tidyverse
|
| 1248 |
+
timechange
|
| 1249 |
+
timeDate
|
| 1250 |
+
tinytex
|
| 1251 |
+
tools
|
| 1252 |
+
treeio
|
| 1253 |
+
triebeard
|
| 1254 |
+
TTR
|
| 1255 |
+
tweenr
|
| 1256 |
+
tximport
|
| 1257 |
+
tzdb
|
| 1258 |
+
UCSC.utils
|
| 1259 |
+
urltools
|
| 1260 |
+
utf8
|
| 1261 |
+
utils
|
| 1262 |
+
uuid
|
| 1263 |
+
vctrs
|
| 1264 |
+
viridisLite
|
| 1265 |
+
vroom
|
| 1266 |
+
withr
|
| 1267 |
+
xfun
|
| 1268 |
+
xml2
|
| 1269 |
+
xtable
|
| 1270 |
+
xts
|
| 1271 |
+
XVector
|
| 1272 |
+
yaml
|
| 1273 |
+
yulab.utils
|
| 1274 |
+
zoo
|
| 1275 |
+
|
| 1276 |
+
|
| 1277 |
+
Searching for clusterProfiler or similar...
|
| 1278 |
+
KEGGREST
|
| 1279 |
+
</observation>
|
| 1280 |
+
|
| 1281 |
+
================================== Ai Message ==================================
|
| 1282 |
+
|
| 1283 |
+
The `clusterProfiler` package is not installed. I have `KEGGREST`, `DOSE`, `fgsea`, and `org.Mm.eg.db` available. Let me perform KEGG enrichment using KEGGREST and a hypergeometric test manually.
|
| 1284 |
+
|
| 1285 |
+
**Plan:**
|
| 1286 |
+
1. [✓] Examine the data and prepare count files and metadata for each mouse model
|
| 1287 |
+
2. [✓] Run DESeq2 for 5xFAD model (GSE168137)
|
| 1288 |
+
3. [✓] Run DESeq2 for 3xTg-AD model (GSE161904)
|
| 1289 |
+
4. [✓] Use pre-computed DEA for PS3O1S
|
| 1290 |
+
5. [✓] Convert gene IDs to Entrez for KEGG enrichment
|
| 1291 |
+
6. [ ] Run KEGG enrichment for all three models using KEGGREST + hypergeometric test
|
| 1292 |
+
7. [ ] Combine results into final CSV with shared pathways
|
| 1293 |
+
|
| 1294 |
+
<execute>
|
| 1295 |
+
#!R
|
| 1296 |
+
# Use KEGGREST to perform KEGG pathway enrichment analysis
|
| 1297 |
+
library(KEGGREST)
|
| 1298 |
+
library(org.Mm.eg.db)
|
| 1299 |
+
|
| 1300 |
+
setwd('/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905')
|
| 1301 |
+
|
| 1302 |
+
# Read Entrez IDs
|
| 1303 |
+
entrez5 <- readLines('entrez_5xFAD.txt')
|
| 1304 |
+
entrez3 <- readLines('entrez_3xTgAD.txt')
|
| 1305 |
+
entrez_ps3 <- readLines('entrez_PS3O1S.txt')
|
| 1306 |
+
|
| 1307 |
+
cat('5xFAD entrez count:', length(entrez5), '\n')
|
| 1308 |
+
cat('3xTgAD entrez count:', length(entrez3), '\n')
|
| 1309 |
+
cat('PS3O1S entrez count:', length(entrez_ps3), '\n')
|
| 1310 |
+
|
| 1311 |
+
# Get all mouse KEGG pathways (organism code: mmu)
|
| 1312 |
+
cat('Fetching mouse KEGG pathways...\n')
|
| 1313 |
+
mmu_pathways <- keggList('pathway', 'mmu')
|
| 1314 |
+
cat('Total mouse pathways:', length(mmu_pathways), '\n')
|
| 1315 |
+
|
| 1316 |
+
# Get pathway IDs and names
|
| 1317 |
+
pathway_ids <- names(mmu_pathways)
|
| 1318 |
+
pathway_names <- unname(mmu_pathways)
|
| 1319 |
+
|
| 1320 |
+
# Function to get genes for a given KEGG pathway
|
| 1321 |
+
get_pathway_genes <- function(pid) {
|
| 1322 |
+
tryCatch({
|
| 1323 |
+
pw <- keggGet(pid)
|
| 1324 |
+
if (!is.null(pw[[1]]$GENE)) {
|
| 1325 |
+
genes <- pw[[1]]$GENE
|
| 1326 |
+
# KEGG returns genes in format: "ENTREZID GeneName"
|
| 1327 |
+
entrez_ids <- genes[seq(1, length(genes), 2)]
|
| 1328 |
+
return(entrez_ids)
|
| 1329 |
+
} else {
|
| 1330 |
+
return(NULL)
|
| 1331 |
+
}
|
| 1332 |
+
}, error = function(e) {
|
| 1333 |
+
return(NULL)
|
| 1334 |
+
})
|
| 1335 |
+
}
|
| 1336 |
+
|
| 1337 |
+
# Get all pathway-gene mappings
|
| 1338 |
+
cat('Fetching pathway gene lists...\n')
|
| 1339 |
+
pathway_genes <- list()
|
| 1340 |
+
pathway_desc <- list()
|
| 1341 |
+
|
| 1342 |
+
for (i in seq_along(pathway_ids)) {
|
| 1343 |
+
pid <- pathway_ids[i]
|
| 1344 |
+
pname <- pathway_names[i]
|
| 1345 |
+
if (i %% 20 == 0) cat(' Processing pathway', i, 'of', length(pathway_ids), '\n')
|
| 1346 |
+
|
| 1347 |
+
genes <- get_pathway_genes(pid)
|
| 1348 |
+
if (!is.null(genes)) {
|
| 1349 |
+
pathway_genes[[pid]] <- genes
|
| 1350 |
+
pathway_desc[[pid]] <- pname
|
| 1351 |
+
}
|
| 1352 |
+
}
|
| 1353 |
+
|
| 1354 |
+
cat('Pathways with gene mappings:', length(pathway_genes), '\n')
|
| 1355 |
+
|
| 1356 |
+
# Define the background (all genes in the genome) - use all mouse genes from org.Mm.eg.db
|
| 1357 |
+
background <- keys(org.Mm.eg.db, keytype='ENTREZID')
|
| 1358 |
+
cat('Background gene count:', length(background), '\n')
|
| 1359 |
+
|
| 1360 |
+
# Hypergeometric test function
|
| 1361 |
+
enrichment_test <- function(sig_genes, pathway_genes, background_genes) {
|
| 1362 |
+
pvalues <- sapply(pathway_genes, function(pw_genes) {
|
| 1363 |
+
# Intersection of significant genes with pathway genes
|
| 1364 |
+
x <- sum(sig_genes %in% pw_genes)
|
| 1365 |
+
# Total pathway genes in background
|
| 1366 |
+
m <- sum(pw_genes %in% background_genes)
|
| 1367 |
+
# Significant genes
|
| 1368 |
+
k <- length(sig_genes)
|
| 1369 |
+
# Background size
|
| 1370 |
+
n <- length(background_genes)
|
| 1371 |
+
|
| 1372 |
+
if (x > 0 && m > 0) {
|
| 1373 |
+
# Hypergeometric test (phyper: P(X >= x))
|
| 1374 |
+
pval <- phyper(x - 1, m, n - m, k, lower.tail = FALSE)
|
| 1375 |
+
return(pval)
|
| 1376 |
+
} else {
|
| 1377 |
+
return(1.0)
|
| 1378 |
+
}
|
| 1379 |
+
})
|
| 1380 |
+
return(pvalues)
|
| 1381 |
+
}
|
| 1382 |
+
|
| 1383 |
+
# Run enrichment for all three models
|
| 1384 |
+
cat('\n=== Running enrichment for 5xFAD ===\n')
|
| 1385 |
+
pvals5 <- enrichment_test(entrez5, pathway_genes, background)
|
| 1386 |
+
pvals5_adj <- p.adjust(pvals5, method='BH')
|
| 1387 |
+
|
| 1388 |
+
cat('5xFAD enriched pathways (p<0.05):', sum(pvals5 < 0.05), '\n')
|
| 1389 |
+
cat('5xFAD enriched pathways (adj.p<0.05):', sum(pvals5_adj < 0.05), '\n')
|
| 1390 |
+
|
| 1391 |
+
cat('\n=== Running enrichment for 3xTgAD ===\n')
|
| 1392 |
+
pvals3 <- enrichment_test(entrez3, pathway_genes, background)
|
| 1393 |
+
pvals3_adj <- p.adjust(pvals3, method='BH')
|
| 1394 |
+
|
| 1395 |
+
cat('3xTgAD enriched pathways (p<0.05):', sum(pvals3 < 0.05), '\n')
|
| 1396 |
+
|
| 1397 |
+
cat('\n=== Running enrichment for PS3O1S ===\n')
|
| 1398 |
+
pvals_ps3 <- enrichment_test(entrez_ps3, pathway_genes, background)
|
| 1399 |
+
pvals_ps3_adj <- p.adjust(pvals_ps3, method='BH')
|
| 1400 |
+
|
| 1401 |
+
cat('PS3O1S enriched pathways (p<0.05):', sum(pvals_ps3 < 0.05), '\n')
|
| 1402 |
+
|
| 1403 |
+
# Save results
|
| 1404 |
+
results_df <- data.frame(
|
| 1405 |
+
pathway_id = names(pvals5),
|
| 1406 |
+
pathway_name = unlist(pathway_desc[names(pvals5)]),
|
| 1407 |
+
pval_5xFAD = pvals5,
|
| 1408 |
+
adj_pval_5xFAD = pvals5_adj,
|
| 1409 |
+
pval_3xTgAD = pvals3[names(pvals5)],
|
| 1410 |
+
adj_pval_3xTgAD = pvals3_adj[names(pvals5)],
|
| 1411 |
+
pval_PS3O1S = pvals_ps3[names(pvals5)],
|
| 1412 |
+
adj_pval_PS3O1S = pvals_ps3_adj[names(pvals5)]
|
| 1413 |
+
)
|
| 1414 |
+
|
| 1415 |
+
write.csv(results_df, 'kegg_all_pathways.csv', row.names=FALSE)
|
| 1416 |
+
cat('\nFull results saved to kegg_all_pathways.csv\n')
|
| 1417 |
+
cat('Total pathways tested:', nrow(results_df), '\n')
|
| 1418 |
+
</execute>
|
| 1419 |
+
|
| 1420 |
+
================================== Ai Message ==================================
|
| 1421 |
+
|
| 1422 |
+
<observation>Error running R code:
|
| 1423 |
+
Loading required package: AnnotationDbi
|
| 1424 |
+
Loading required package: stats4
|
| 1425 |
+
Loading required package: BiocGenerics
|
| 1426 |
+
Loading required package: generics
|
| 1427 |
+
|
| 1428 |
+
Attaching package: ‘generics’
|
| 1429 |
+
|
| 1430 |
+
The following objects are masked from ‘package:base’:
|
| 1431 |
+
|
| 1432 |
+
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
|
| 1433 |
+
setequal, union
|
| 1434 |
+
|
| 1435 |
+
|
| 1436 |
+
Attaching package: ‘BiocGenerics’
|
| 1437 |
+
|
| 1438 |
+
The following objects are masked from ‘package:stats’:
|
| 1439 |
+
|
| 1440 |
+
IQR, mad, sd, var, xtabs
|
| 1441 |
+
|
| 1442 |
+
The following objects are masked from ‘package:base’:
|
| 1443 |
+
|
| 1444 |
+
anyDuplicated, aperm, append, as.data.frame, basename, cbind,
|
| 1445 |
+
colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
|
| 1446 |
+
get, grep, grepl, is.unsorted, lapply, Map, mapply, match, mget,
|
| 1447 |
+
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
|
| 1448 |
+
rbind, Reduce, rownames, sapply, saveRDS, table, tapply, unique,
|
| 1449 |
+
unsplit, which.max, which.min
|
| 1450 |
+
|
| 1451 |
+
Loading required package: Biobase
|
| 1452 |
+
Welcome to Bioconductor
|
| 1453 |
+
|
| 1454 |
+
Vignettes contain introductory material; view with
|
| 1455 |
+
'browseVignettes()'. To cite Bioconductor, see
|
| 1456 |
+
'citation("Biobase")', and for packages 'citation("pkgname")'.
|
| 1457 |
+
|
| 1458 |
+
Loading required package: IRanges
|
| 1459 |
+
Loading required package: S4Vectors
|
| 1460 |
+
|
| 1461 |
+
Attaching package: ‘S4Vectors’
|
| 1462 |
+
|
| 1463 |
+
The following object is masked from ‘package:utils’:
|
| 1464 |
+
|
| 1465 |
+
findMatches
|
| 1466 |
+
|
| 1467 |
+
The following objects are masked from ‘package:base’:
|
| 1468 |
+
|
| 1469 |
+
expand.grid, I, unname
|
| 1470 |
+
|
| 1471 |
+
|
| 1472 |
+
Error in file(con, "r") : cannot open the connection
|
| 1473 |
+
Calls: readLines -> file
|
| 1474 |
+
In addition: Warning message:
|
| 1475 |
+
In file(con, "r") :
|
| 1476 |
+
cannot open file 'entrez_5xFAD.txt': No such file or directory
|
| 1477 |
+
Execution halted
|
| 1478 |
+
</observation>
|
| 1479 |
+
|
| 1480 |
+
================================== Ai Message ==================================
|
| 1481 |
+
|
| 1482 |
+
<execute>
|
| 1483 |
+
#!BASH
|
| 1484 |
+
echo "Looking for the Entrez list files..."
|
| 1485 |
+
find /225040511/project/ -name "entrez_*" -type f 2>/dev/null
|
| 1486 |
+
echo ""
|
| 1487 |
+
echo "Checking scripts directory..."
|
| 1488 |
+
ls -la /225040511/project/Biomni/experiments/bioagent_bench/scripts/entrez_*
|
| 1489 |
+
</execute>
|
| 1490 |
+
|
| 1491 |
+
================================== Ai Message ==================================
|
| 1492 |
+
|
| 1493 |
+
<observation>Looking for the Entrez list files...
|
| 1494 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_500/alzheimer-mouse_20260515_093531/entrez_ps3o1s.csv
|
| 1495 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_500/alzheimer-mouse_20260515_093531/entrez_5xfad.csv
|
| 1496 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_500/alzheimer-mouse_20260515_093531/entrez_3xtg.csv
|
| 1497 |
+
/225040511/project/Biomni/experiments/bioagent_bench/scripts/entrez_PS3O1S.txt
|
| 1498 |
+
/225040511/project/Biomni/experiments/bioagent_bench/scripts/entrez_3xTgAD.txt
|
| 1499 |
+
/225040511/project/Biomni/experiments/bioagent_bench/scripts/entrez_5xFAD.txt
|
| 1500 |
+
|
| 1501 |
+
Checking scripts directory...
|
| 1502 |
+
-rw-r--r-- 1 root root 3251 May 15 13:53 /225040511/project/Biomni/experiments/bioagent_bench/scripts/entrez_3xTgAD.txt
|
| 1503 |
+
-rw-r--r-- 1 root root 5495 May 15 13:53 /225040511/project/Biomni/experiments/bioagent_bench/scripts/entrez_5xFAD.txt
|
| 1504 |
+
-rw-r--r-- 1 root root 4140 May 15 13:53 /225040511/project/Biomni/experiments/bioagent_bench/scripts/entrez_PS3O1S.txt
|
| 1505 |
+
</observation>
|
| 1506 |
+
|
| 1507 |
+
================================== Ai Message ==================================
|
| 1508 |
+
|
| 1509 |
+
The working directory issue persists - R writes to the scripts directory. Let me copy the needed files and run the KEGG enrichment properly.
|
| 1510 |
+
|
| 1511 |
+
<execute>
|
| 1512 |
+
#!BASH
|
| 1513 |
+
echo "Copying entrez files to run directory..."
|
| 1514 |
+
cp /225040511/project/Biomni/experiments/bioagent_bench/scripts/entrez_*.txt /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/
|
| 1515 |
+
echo "Done. Files in run directory:"
|
| 1516 |
+
ls -la /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/entrez_*
|
| 1517 |
+
</execute>
|
| 1518 |
+
|
| 1519 |
+
================================== Ai Message ==================================
|
| 1520 |
+
|
| 1521 |
+
<observation>Copying entrez files to run directory...
|
| 1522 |
+
Done. Files in run directory:
|
| 1523 |
+
-rw-r--r-- 1 root root 3251 May 15 13:53 /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/entrez_3xTgAD.txt
|
| 1524 |
+
-rw-r--r-- 1 root root 5495 May 15 13:53 /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/entrez_5xFAD.txt
|
| 1525 |
+
-rw-r--r-- 1 root root 4140 May 15 13:53 /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/entrez_PS3O1S.txt
|
| 1526 |
+
</observation>
|
| 1527 |
+
|
| 1528 |
+
================================== Ai Message ==================================
|
| 1529 |
+
|
| 1530 |
+
<execute>
|
| 1531 |
+
#!R
|
| 1532 |
+
# Use KEGGREST to perform KEGG pathway enrichment analysis
|
| 1533 |
+
library(KEGGREST)
|
| 1534 |
+
library(org.Mm.eg.db)
|
| 1535 |
+
|
| 1536 |
+
run_dir <- '/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905'
|
| 1537 |
+
|
| 1538 |
+
# Read Entrez IDs
|
| 1539 |
+
entrez5 <- readLines(file.path(run_dir, 'entrez_5xFAD.txt'))
|
| 1540 |
+
entrez3 <- readLines(file.path(run_dir, 'entrez_3xTgAD.txt'))
|
| 1541 |
+
entrez_ps3 <- readLines(file.path(run_dir, 'entrez_PS3O1S.txt'))
|
| 1542 |
+
|
| 1543 |
+
cat('5xFAD entrez count:', length(entrez5), '\n')
|
| 1544 |
+
cat('3xTgAD entrez count:', length(entrez3), '\n')
|
| 1545 |
+
cat('PS3O1S entrez count:', length(entrez_ps3), '\n')
|
| 1546 |
+
|
| 1547 |
+
# Get all mouse KEGG pathways (organism code: mmu)
|
| 1548 |
+
cat('Fetching mouse KEGG pathways...\n')
|
| 1549 |
+
mmu_pathways <- keggList('pathway', 'mmu')
|
| 1550 |
+
cat('Total mouse pathways:', length(mmu_pathways), '\n')
|
| 1551 |
+
|
| 1552 |
+
# Get pathway IDs and names
|
| 1553 |
+
pathway_ids <- names(mmu_pathways)
|
| 1554 |
+
pathway_names <- unname(mmu_pathways)
|
| 1555 |
+
|
| 1556 |
+
# Function to get genes for a given KEGG pathway
|
| 1557 |
+
get_pathway_genes <- function(pid) {
|
| 1558 |
+
tryCatch({
|
| 1559 |
+
pw <- keggGet(pid)
|
| 1560 |
+
if (!is.null(pw[[1]]$GENE)) {
|
| 1561 |
+
genes <- pw[[1]]$GENE
|
| 1562 |
+
# KEGG returns genes in format: "ENTREZID GeneName"
|
| 1563 |
+
entrez_ids <- genes[seq(1, length(genes), 2)]
|
| 1564 |
+
return(entrez_ids)
|
| 1565 |
+
} else {
|
| 1566 |
+
return(NULL)
|
| 1567 |
+
}
|
| 1568 |
+
}, error = function(e) {
|
| 1569 |
+
return(NULL)
|
| 1570 |
+
})
|
| 1571 |
+
}
|
| 1572 |
+
|
| 1573 |
+
# Get all pathway-gene mappings
|
| 1574 |
+
cat('Fetching pathway gene lists...\n')
|
| 1575 |
+
pathway_genes <- list()
|
| 1576 |
+
pathway_desc <- list()
|
| 1577 |
+
|
| 1578 |
+
for (i in seq_along(pathway_ids)) {
|
| 1579 |
+
pid <- pathway_ids[i]
|
| 1580 |
+
pname <- pathway_names[i]
|
| 1581 |
+
if (i %% 20 == 0) cat(' Processing pathway', i, 'of', length(pathway_ids), '\n')
|
| 1582 |
+
|
| 1583 |
+
genes <- get_pathway_genes(pid)
|
| 1584 |
+
if (!is.null(genes)) {
|
| 1585 |
+
pathway_genes[[pid]] <- genes
|
| 1586 |
+
pathway_desc[[pid]] <- pname
|
| 1587 |
+
}
|
| 1588 |
+
}
|
| 1589 |
+
|
| 1590 |
+
cat('Pathways with gene mappings:', length(pathway_genes), '\n')
|
| 1591 |
+
|
| 1592 |
+
# Define the background (all mouse genes)
|
| 1593 |
+
background <- keys(org.Mm.eg.db, keytype='ENTREZID')
|
| 1594 |
+
cat('Background gene count:', length(background), '\n')
|
| 1595 |
+
|
| 1596 |
+
# Hypergeometric test function
|
| 1597 |
+
enrichment_test <- function(sig_genes, pathway_genes, background_genes) {
|
| 1598 |
+
pvalues <- sapply(pathway_genes, function(pw_genes) {
|
| 1599 |
+
x <- sum(sig_genes %in% pw_genes)
|
| 1600 |
+
m <- sum(pw_genes %in% background_genes)
|
| 1601 |
+
k <- length(sig_genes)
|
| 1602 |
+
n <- length(background_genes)
|
| 1603 |
+
|
| 1604 |
+
if (x > 0 && m > 0) {
|
| 1605 |
+
pval <- phyper(x - 1, m, n - m, k, lower.tail = FALSE)
|
| 1606 |
+
return(pval)
|
| 1607 |
+
} else {
|
| 1608 |
+
return(1.0)
|
| 1609 |
+
}
|
| 1610 |
+
})
|
| 1611 |
+
return(pvalues)
|
| 1612 |
+
}
|
| 1613 |
+
|
| 1614 |
+
# Run enrichment for all three models
|
| 1615 |
+
cat('\n=== Running enrichment for all models ===\n')
|
| 1616 |
+
pvals5 <- enrichment_test(entrez5, pathway_genes, background)
|
| 1617 |
+
pvals3 <- enrichment_test(entrez3, pathway_genes, background)
|
| 1618 |
+
pvals_ps3 <- enrichment_test(entrez_ps3, pathway_genes, background)
|
| 1619 |
+
|
| 1620 |
+
cat('5xFAD enriched pathways (p<0.05):', sum(pvals5 < 0.05), '\n')
|
| 1621 |
+
cat('3xTgAD enriched pathways (p<0.05):', sum(pvals3 < 0.05), '\n')
|
| 1622 |
+
cat('PS3O1S enriched pathways (p<0.05):', sum(pvals_ps3 < 0.05), '\n')
|
| 1623 |
+
|
| 1624 |
+
# Save results
|
| 1625 |
+
results_df <- data.frame(
|
| 1626 |
+
pathway_id = names(pathway_genes),
|
| 1627 |
+
pathway_name = unlist(pathway_desc[names(pathway_genes)]),
|
| 1628 |
+
pval_5xFAD = pvals5[names(pathway_genes)],
|
| 1629 |
+
pval_3xTgAD = pvals3[names(pathway_genes)],
|
| 1630 |
+
pval_PS3O1S = pvals_ps3[names(pathway_genes)]
|
| 1631 |
+
)
|
| 1632 |
+
|
| 1633 |
+
write.csv(results_df, file.path(run_dir, 'kegg_all_pathways.csv'), row.names=FALSE)
|
| 1634 |
+
cat('\nFull results saved to kegg_all_pathways.csv\n')
|
| 1635 |
+
cat('Total pathways tested:', nrow(results_df), '\n')
|
| 1636 |
+
|
| 1637 |
+
# Show top 10 pathways for each model
|
| 1638 |
+
cat('\n=== Top 10 pathways for 5xFAD ===\n')
|
| 1639 |
+
idx5 <- order(pvals5)[1:10]
|
| 1640 |
+
for (i in idx5) {
|
| 1641 |
+
cat(sprintf(' %s - %s: p=%.6f\n', names(pathway_genes)[i], pathway_desc[[names(pathway_genes)[i]]], pvals5[i]))
|
| 1642 |
+
}
|
| 1643 |
+
|
| 1644 |
+
cat('\n=== Top 10 pathways for 3xTgAD ===\n')
|
| 1645 |
+
idx3 <- order(pvals3)[1:10]
|
| 1646 |
+
for (i in idx3) {
|
| 1647 |
+
cat(sprintf(' %s - %s: p=%.6f\n', names(pathway_genes)[i], pathway_desc[[names(pathway_genes)[i]]], pvals3[i]))
|
| 1648 |
+
}
|
| 1649 |
+
|
| 1650 |
+
cat('\n=== Top 10 pathways for PS3O1S ===\n')
|
| 1651 |
+
idx_ps3 <- order(pvals_ps3)[1:10]
|
| 1652 |
+
for (i in idx_ps3) {
|
| 1653 |
+
cat(sprintf(' %s - %s: p=%.6f\n', names(pathway_genes)[i], pathway_desc[[names(pathway_genes)[i]]], pvals_ps3[i]))
|
| 1654 |
+
}
|
| 1655 |
+
</execute>
|
| 1656 |
+
|
| 1657 |
+
================================== Ai Message ==================================
|
| 1658 |
+
|
| 1659 |
+
<observation>5xFAD entrez count: 873
|
| 1660 |
+
3xTgAD entrez count: 485
|
| 1661 |
+
PS3O1S entrez count: 633
|
| 1662 |
+
Fetching mouse KEGG pathways...
|
| 1663 |
+
Total mouse pathways: 367
|
| 1664 |
+
Fetching pathway gene lists...
|
| 1665 |
+
Processing pathway 20 of 367
|
| 1666 |
+
Processing pathway 40 of 367
|
| 1667 |
+
Processing pathway 60 of 367
|
| 1668 |
+
Processing pathway 80 of 367
|
| 1669 |
+
Processing pathway 100 of 367
|
| 1670 |
+
Processing pathway 120 of 367
|
| 1671 |
+
Processing pathway 140 of 367
|
| 1672 |
+
Processing pathway 160 of 367
|
| 1673 |
+
Processing pathway 180 of 367
|
| 1674 |
+
Processing pathway 200 of 367
|
| 1675 |
+
Processing pathway 220 of 367
|
| 1676 |
+
Processing pathway 240 of 367
|
| 1677 |
+
Processing pathway 260 of 367
|
| 1678 |
+
Processing pathway 280 of 367
|
| 1679 |
+
Processing pathway 300 of 367
|
| 1680 |
+
Processing pathway 320 of 367
|
| 1681 |
+
Processing pathway 340 of 367
|
| 1682 |
+
Processing pathway 360 of 367
|
| 1683 |
+
Pathways with gene mappings: 354
|
| 1684 |
+
Background gene count: 112254
|
| 1685 |
+
|
| 1686 |
+
=== Running enrichment for all models ===
|
| 1687 |
+
5xFAD enriched pathways (p<0.05): 248
|
| 1688 |
+
3xTgAD enriched pathways (p<0.05): 126
|
| 1689 |
+
PS3O1S enriched pathways (p<0.05): 164
|
| 1690 |
+
|
| 1691 |
+
Full results saved to kegg_all_pathways.csv
|
| 1692 |
+
Total pathways tested: 354
|
| 1693 |
+
|
| 1694 |
+
=== Top 10 pathways for 5xFAD ===
|
| 1695 |
+
mmu05168 - Herpes simplex virus 1 infection - Mus musculus (house mouse): p=0.000000
|
| 1696 |
+
mmu05169 - Epstein-Barr virus infection - Mus musculus (house mouse): p=0.000000
|
| 1697 |
+
mmu05164 - Influenza A - Mus musculus (house mouse): p=0.000000
|
| 1698 |
+
mmu05152 - Tuberculosis - Mus musculus (house mouse): p=0.000000
|
| 1699 |
+
mmu04145 - Phagosome - Mus musculus (house mouse): p=0.000000
|
| 1700 |
+
mmu04380 - Osteoclast differentiation - Mus musculus (house mouse): p=0.000000
|
| 1701 |
+
mmu04060 - Cytokine-cytokine receptor interaction - Mus musculus (house mouse): p=0.000000
|
| 1702 |
+
mmu04142 - Lysosome biogenesis - Mus musculus (house mouse): p=0.000000
|
| 1703 |
+
mmu05140 - Leishmaniasis - Mus musculus (house mouse): p=0.000000
|
| 1704 |
+
mmu04621 - NOD-like receptor signaling pathway - Mus musculus (house mouse): p=0.000000
|
| 1705 |
+
|
| 1706 |
+
=== Top 10 pathways for 3xTgAD ===
|
| 1707 |
+
mmu04024 - cAMP signaling pathway - Mus musculus (house mouse): p=0.000000
|
| 1708 |
+
mmu04082 - Neuroactive ligand signaling - Mus musculus (house mouse): p=0.000000
|
| 1709 |
+
mmu04080 - Neuroactive ligand-receptor interaction - Mus musculus (house mouse): p=0.000000
|
| 1710 |
+
mmu04081 - Hormone signaling - Mus musculus (house mouse): p=0.000000
|
| 1711 |
+
mmu00590 - Arachidonic acid metabolism - Mus musculus (house mouse): p=0.000000
|
| 1712 |
+
mmu05200 - Pathways in cancer - Mus musculus (house mouse): p=0.000001
|
| 1713 |
+
mmu04380 - Osteoclast differentiation - Mus musculus (house mouse): p=0.000002
|
| 1714 |
+
mmu05030 - Cocaine addiction - Mus musculus (house mouse): p=0.000002
|
| 1715 |
+
mmu04519 - Cadherin signaling - Mus musculus (house mouse): p=0.000002
|
| 1716 |
+
mmu04270 - Vascular smooth muscle contraction - Mus musculus (house mouse): p=0.000004
|
| 1717 |
+
|
| 1718 |
+
=== Top 10 pathways for PS3O1S ===
|
| 1719 |
+
mmu04082 - Neuroactive ligand signaling - Mus musculus (house mouse): p=0.000000
|
| 1720 |
+
mmu04142 - Lysosome biogenesis - Mus musculus (house mouse): p=0.000000
|
| 1721 |
+
mmu04141 - Protein processing in endoplasmic reticulum - Mus musculus (house mouse): p=0.000000
|
| 1722 |
+
mmu04081 - Hormone signaling - Mus musculus (house mouse): p=0.000000
|
| 1723 |
+
mmu04519 - Cadherin signaling - Mus musculus (house mouse): p=0.000000
|
| 1724 |
+
mmu04390 - Hippo signaling pathway - Mus musculus (house mouse): p=0.000000
|
| 1725 |
+
mmu04724 - Glutamatergic synapse - Mus musculus (house mouse): p=0.000000
|
| 1726 |
+
mmu04080 - Neuroactive ligand-receptor interaction - Mus musculus (house mouse): p=0.000001
|
| 1727 |
+
mmu04024 - cAMP signaling pathway - Mus musculus (house mouse): p=0.000001
|
| 1728 |
+
mmu05165 - Human papillomavirus infection - Mus musculus (house mouse): p=0.000001
|
| 1729 |
+
</observation>
|
| 1730 |
+
|
| 1731 |
+
================================== Ai Message ==================================
|
| 1732 |
+
|
| 1733 |
+
Excellent! The KEGG enrichment analysis is complete. Now let me generate the final output CSV.
|
| 1734 |
+
|
| 1735 |
+
**Plan:**
|
| 1736 |
+
1. [✓] Examine the data and prepare count files and metadata for each mouse model
|
| 1737 |
+
2. [✓] Run DESeq2 for 5xFAD model (GSE168137)
|
| 1738 |
+
3. [✓] Run DESeq2 for 3xTg-AD model (GSE161904)
|
| 1739 |
+
4. [✓] Use pre-computed DEA for PS3O1S
|
| 1740 |
+
5. [✓] Convert gene IDs to Entrez for KEGG enrichment
|
| 1741 |
+
6. [✓] Run KEGG enrichment for all three models using KEGGREST + hypergeometric test
|
| 1742 |
+
7. [ ] Combine results into final CSV with shared pathways in the required format
|
| 1743 |
+
|
| 1744 |
+
<execute>
|
| 1745 |
+
#!R
|
| 1746 |
+
# Generate the final pathway_comparison.csv in the exact required format
|
| 1747 |
+
setwd('/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905')
|
| 1748 |
+
|
| 1749 |
+
# Read the full results
|
| 1750 |
+
results_df <- read.csv('kegg_all_pathways.csv')
|
| 1751 |
+
cat('Total pathways:', nrow(results_df), '\n')
|
| 1752 |
+
cat('Columns:', colnames(results_df), '\n')
|
| 1753 |
+
|
| 1754 |
+
# Format the pathway column as: "PathwayName Mus musculus mmuXXXXX" (matching example format)
|
| 1755 |
+
results_df$pathway <- paste0(
|
| 1756 |
+
results_df$pathway_name,
|
| 1757 |
+
' Mus musculus ',
|
| 1758 |
+
results_df$pathway_id
|
| 1759 |
+
)
|
| 1760 |
+
|
| 1761 |
+
# Create the output with required column names
|
| 1762 |
+
output <- data.frame(
|
| 1763 |
+
Pathway = results_df$pathway,
|
| 1764 |
+
`5xFAD_pvalue` = results_df$pval_5xFAD,
|
| 1765 |
+
`3xTg_AD_pvalue` = results_df$pval_3xTgAD,
|
| 1766 |
+
`PS3O1S_pvalue` = results_df$pval_PS3O1S,
|
| 1767 |
+
check.names = FALSE # preserve column names with special characters
|
| 1768 |
+
)
|
| 1769 |
+
|
| 1770 |
+
# Write output
|
| 1771 |
+
write.csv(output, 'pathway_comparison.csv', row.names=FALSE)
|
| 1772 |
+
cat('Final output written to pathway_comparison.csv\n')
|
| 1773 |
+
cat('Number of rows:', nrow(output), '\n')
|
| 1774 |
+
|
| 1775 |
+
# Show first few rows
|
| 1776 |
+
cat('\n=== First 10 rows ===\n')
|
| 1777 |
+
print(head(output, 10))
|
| 1778 |
+
|
| 1779 |
+
# Show number of shared significant pathways (p<0.05 across all three)
|
| 1780 |
+
cat('\n=== Shared significant pathways (p<0.05 in ALL models) ===\n')
|
| 1781 |
+
shared_sig <- output[output$`5xFAD_pvalue` < 0.05 & output$`3xTg_AD_pvalue` < 0.05 & output$PS3O1S_pvalue < 0.05, ]
|
| 1782 |
+
cat('Number of shared significant pathways:', nrow(shared_sig), '\n')
|
| 1783 |
+
if (nrow(shared_sig) > 0) {
|
| 1784 |
+
print(shared_sig)
|
| 1785 |
+
}
|
| 1786 |
+
</execute>
|
| 1787 |
+
|
| 1788 |
+
================================== Ai Message ==================================
|
| 1789 |
+
|
| 1790 |
+
<observation>The output is too long to be added to context. Here are the first 10K characters...
|
| 1791 |
+
Total pathways: 354
|
| 1792 |
+
Columns: pathway_id pathway_name pval_5xFAD pval_3xTgAD pval_PS3O1S
|
| 1793 |
+
Final output written to pathway_comparison.csv
|
| 1794 |
+
Number of rows: 354
|
| 1795 |
+
|
| 1796 |
+
=== First 10 rows ===
|
| 1797 |
+
Pathway
|
| 1798 |
+
1 Glycolysis / Gluconeogenesis - Mus musculus (house mouse) Mus musculus mmu00010
|
| 1799 |
+
2 Citrate cycle (TCA cycle) - Mus musculus (house mouse) Mus musculus mmu00020
|
| 1800 |
+
3 Pentose phosphate pathway - Mus musculus (house mouse) Mus musculus mmu00030
|
| 1801 |
+
4 Pentose and glucuronate interconversions - Mus musculus (house mouse) Mus musculus mmu00040
|
| 1802 |
+
5 Fructose and mannose metabolism - Mus musculus (house mouse) Mus musculus mmu00051
|
| 1803 |
+
6 Galactose metabolism - Mus musculus (house mouse) Mus musculus mmu00052
|
| 1804 |
+
7 Ascorbate and aldarate metabolism - Mus musculus (house mouse) Mus musculus mmu00053
|
| 1805 |
+
8 Starch and sucrose metabolism - Mus musculus (house mouse) Mus musculus mmu00500
|
| 1806 |
+
9 Pyruvate metabolism - Mus musculus (house mouse) Mus musculus mmu00620
|
| 1807 |
+
10 Glyoxylate and dicarboxylate metabolism - Mus musculus (house mouse) Mus musculus mmu00630
|
| 1808 |
+
5xFAD_pvalue 3xTg_AD_pvalue PS3O1S_pvalue
|
| 1809 |
+
1 0.0018887625 0.25187866 0.31545016
|
| 1810 |
+
2 1.0000000000 1.00000000 0.16555101
|
| 1811 |
+
3 1.0000000000 1.00000000 0.17493810
|
| 1812 |
+
4 0.0029912021 1.00000000 0.18882141
|
| 1813 |
+
5 0.0029912021 1.00000000 1.00000000
|
| 1814 |
+
6 0.0001098547 1.00000000 0.16555101
|
| 1815 |
+
7 0.0256849798 0.12940343 1.00000000
|
| 1816 |
+
8 0.0303455209 1.00000000 1.00000000
|
| 1817 |
+
9 0.0460988637 0.01563373 0.02569132
|
| 1818 |
+
10 0.2271584385 1.00000000 0.01493350
|
| 1819 |
+
|
| 1820 |
+
=== Shared significant pathways (p<0.05 in ALL models) ===
|
| 1821 |
+
Number of shared significant pathways: 72
|
| 1822 |
+
Pathway
|
| 1823 |
+
9 Pyruvate metabolism - Mus musculus (house mouse) Mus musculus mmu00620
|
| 1824 |
+
25 Glycerophospholipid metabolism - Mus musculus (house mouse) Mus musculus mmu00564
|
| 1825 |
+
26 Ether lipid metabolism - Mus musculus (house mouse) Mus musculus mmu00565
|
| 1826 |
+
27 Sphingolipid metabolism - Mus musculus (house mouse) Mus musculus mmu00600
|
| 1827 |
+
98 Ubiquitin mediated proteolysis - Mus musculus (house mouse) Mus musculus mmu04120
|
| 1828 |
+
111 Viral life cycle - HIV-1 - Mus musculus (house mouse) Mus musculus mmu03250
|
| 1829 |
+
121 MAPK signaling pathway - Mus musculus (house mouse) Mus musculus mmu04010
|
| 1830 |
+
123 Ras signaling pathway - Mus musculus (house mouse) Mus musculus mmu04014
|
| 1831 |
+
124 Rap1 signaling pathway - Mus musculus (house mouse) Mus musculus mmu04015
|
| 1832 |
+
125 Wnt signaling pathway - Mus musculus (house mouse) Mus musculus mmu04310
|
| 1833 |
+
131 VEGF signaling pathway - Mus musculus (house mouse) Mus musculus mmu04370
|
| 1834 |
+
132 Apelin signaling pathway - Mus musculus (house mouse) Mus musculus mmu04371
|
| 1835 |
+
138 Calcium signaling pathway - Mus musculus (house mouse) Mus musculus mmu04020
|
| 1836 |
+
140 Phospholipase D signaling pathway - Mus musculus (house mouse) Mus musculus mmu04072
|
| 1837 |
+
142 cAMP signaling pathway - Mus musculus (house mouse) Mus musculus mmu04024
|
| 1838 |
+
144 PI3K-Akt signaling pathway - Mus musculus (house mouse) Mus musculus mmu04151
|
| 1839 |
+
145 AMPK signaling pathway - Mus musculus (house mouse) Mus musculus mmu04152
|
| 1840 |
+
147 Neuroactive ligand-receptor interaction - Mus musculus (house mouse) Mus musculus mmu04080
|
| 1841 |
+
148 Neuroactive ligand signaling - Mus musculus (house mouse) Mus musculus mmu04082
|
| 1842 |
+
149 Hormone signaling - Mus musculus (house mouse) Mus musculus mmu04081
|
| 1843 |
+
150 Cytokine-cytokine receptor interaction - Mus musculus (house mouse) Mus musculus mmu04060
|
| 1844 |
+
151 Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse) Mus musculus mmu04061
|
| 1845 |
+
155 Integrin signaling - Mus musculus (house mouse) Mus musculus mmu04518
|
| 1846 |
+
156 Cadherin signaling - Mus musculus (house mouse) Mus musculus mmu04519
|
| 1847 |
+
157 Endocytosis - Mus musculus (house mouse) Mus musculus mmu04144
|
| 1848 |
+
159 Lysosome biogenesis - Mus musculus (house mouse) Mus musculus mmu04142
|
| 1849 |
+
165 Cell cycle - Mus musculus (house mouse) Mus musculus mmu04110
|
| 1850 |
+
166 Oocyte meiosis - Mus musculus (house mouse) Mus musculus mmu04114
|
| 1851 |
+
167 Apoptosis - Mus musculus (house mouse) Mus musculus mmu04210
|
| 1852 |
+
173 Focal adhesion - Mus musculus (house mouse) Mus musculus mmu04510
|
| 1853 |
+
177 Signaling pathways regulating pluripotency of stem cells - Mus musculus (house mouse) Mus musculus mmu04550
|
| 1854 |
+
179 Cytoskeleton in muscle cells - Mus musculus (house mouse) Mus musculus mmu04820
|
| 1855 |
+
184 Neutrophil extracellular trap formation - Mus musculus (house mouse) Mus musculus mmu04613
|
| 1856 |
+
185 Toll-like receptor signaling pathway - Mus musculus (house mouse) Mus musculus mmu04620
|
| 1857 |
+
198 Fc gamma R-mediated phagosome formation - Mus musculus (house mouse) Mus musculus mmu04666
|
| 1858 |
+
201 Chemokine signaling pathway - Mus musculus (house mouse) Mus musculus mmu04062
|
| 1859 |
+
211 Estrogen signaling pathway - Mus musculus (house mouse) Mus musculus mmu04915
|
| 1860 |
+
214 Oxytocin signaling pathway - Mus musculus (house mouse) Mus musculus mmu04921
|
| 1861 |
+
215 Relaxin signaling pathway - Mus musculus (house mouse) Mus musculus mmu04926
|
| 1862 |
+
216 Growth hormone synthesis, secretion and action - Mus musculus (house mouse) Mus musculus mmu04935
|
| 1863 |
+
217 Thyroid hormone synthesis - Mus musculus (house mouse) Mus musculus mmu04918
|
| 1864 |
+
219 Parathyroid hormone synthesis, secretion and action - Mus musculus (house mouse) Mus musculus mmu04928
|
| 1865 |
+
224 Cortisol synthesis and secretion - Mus musculus (house mouse) Mus musculus mmu04927
|
| 1866 |
+
226 Adrenergic signaling in cardiomyocytes - Mus musculus (house mouse) Mus musculus mmu04261
|
| 1867 |
+
227 Vascular smooth muscle contraction - Mus musculus (house mouse) Mus musculus mmu04270
|
| 1868 |
+
245 Glutamatergic synapse - Mus musculus (house mouse) Mus musculus mmu04724
|
| 1869 |
+
247 Cholinergic synapse - Mus musculus (house mouse) Mus musculus mmu04725
|
| 1870 |
+
248 Dopaminergic synapse - Mus musculus (house mouse) Mus musculus mmu04728
|
| 1871 |
+
249 Serotonergic synapse - Mus musculus (house mouse) Mus musculus mmu04726
|
| 1872 |
+
251 Long-term depression - Mus musculus (house mouse) Mus musculus mmu04730
|
| 1873 |
+
254 Neurotrophin signaling pathway - Mus musculus (house mouse) Mus musculus mmu04722
|
| 1874 |
+
258 Inflammatory mediator regulation of TRP channels - Mus musculus (house mouse) Mus musculus mmu04750
|
| 1875 |
+
267 Pathways in cancer - Mus musculus (house mouse) Mus musculus mmu05200
|
| 1876 |
+
273 Chemical carcinogenesis - reactive oxygen species - Mus musculus (house mouse) Mus musculus mmu05208
|
| 1877 |
+
276 Choline metabolism in cancer - Mus musculus (house mouse) Mus musculus mmu05231
|
| 1878 |
+
280 Hepatocellular carcinoma - Mus musculus (house mouse) Mus musculus mmu05225
|
| 1879 |
+
295 Human T-cell leukemia virus 1 infection - Mus musculus (house mouse) Mus musculus mmu05166
|
| 1880 |
+
296 Human immunodeficiency virus 1 infection - Mus musculus (house mouse) Mus musculus mmu05170
|
| 1881 |
+
301 Measles - Mus musculus (house mouse) Mus musculus mmu05162
|
| 1882 |
+
303 Human cytomegalovirus infection - Mus musculus (house mouse) Mus musculus mmu05163
|
| 1883 |
+
304 Kaposi sarcoma-associated herpesvirus infection - Mus musculus (house mouse) Mus musculus mmu05167
|
| 1884 |
+
305 Epstein-Barr virus infection - Mus musculus (house mouse) Mus musculus mmu05169
|
| 1885 |
+
306 Human papillomavirus infection - Mus musculus (house mouse) Mus musculus mmu05165
|
| 1886 |
+
315 Malaria - Mus musculus (house mouse) Mus musculus mmu05144
|
| 1887 |
+
316 Toxoplasmosis - Mus musculus (house mouse) Mus musculus mmu05145
|
| 1888 |
+
329 Parkinson disease - Mus musculus (house mouse) Mus musculus mmu05012
|
| 1889 |
+
334 Pathways of neurodegeneration - multiple diseases - Mus musculus (house mouse) Mus musculus mmu05022
|
| 1890 |
+
337 Morphine addiction - Mus musculus (house mouse) Mus musculus mmu05032
|
| 1891 |
+
339 Alcoholism - Mus musculus (house mouse) Mus musc</observation>
|
| 1892 |
+
|
| 1893 |
+
================================== Ai Message ==================================
|
| 1894 |
+
|
| 1895 |
+
The pathway name format doesn't match the example. Let me fix the formatting to match exactly.
|
| 1896 |
+
|
| 1897 |
+
<execute>
|
| 1898 |
+
#!R
|
| 1899 |
+
# Fix the pathway name format to match the example
|
| 1900 |
+
# Example: "Phagosome Homo sapiens hsa04145"
|
| 1901 |
+
# We need: "PathwayName Mus musculus mmuXXXXX"
|
| 1902 |
+
|
| 1903 |
+
setwd('/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905')
|
| 1904 |
+
|
| 1905 |
+
results_df <- read.csv('kegg_all_pathways.csv')
|
| 1906 |
+
|
| 1907 |
+
# Extract just the pathway name without "Mus musculus (house mouse)" suffix
|
| 1908 |
+
# pathway_name format: "Glycolysis / Gluconeogenesis - Mus musculus (house mouse)"
|
| 1909 |
+
clean_pathway_name <- gsub(' - Mus musculus \\(house mouse\\)', '', results_df$pathway_name)
|
| 1910 |
+
|
| 1911 |
+
# Format as: "PathwayName Mus musculus mmuXXXXX"
|
| 1912 |
+
clean_pathway <- paste0(clean_pathway_name, ' Mus musculus ', results_df$pathway_id)
|
| 1913 |
+
|
| 1914 |
+
cat('Example pathways:\n')
|
| 1915 |
+
print(head(clean_pathway, 5))
|
| 1916 |
+
|
| 1917 |
+
# Create output
|
| 1918 |
+
output <- data.frame(
|
| 1919 |
+
Pathway = clean_pathway,
|
| 1920 |
+
`5xFAD_pvalue` = results_df$pval_5xFAD,
|
| 1921 |
+
`3xTg_AD_pvalue` = results_df$pval_3xTgAD,
|
| 1922 |
+
`PS3O1S_pvalue` = results_df$pval_PS3O1S,
|
| 1923 |
+
check.names = FALSE
|
| 1924 |
+
)
|
| 1925 |
+
|
| 1926 |
+
write.csv(output, 'pathway_comparison.csv', row.names=FALSE)
|
| 1927 |
+
cat('\nFinal output written to pathway_comparison.csv\n')
|
| 1928 |
+
cat('Number of rows:', nrow(output), '\n')
|
| 1929 |
+
|
| 1930 |
+
# Check specific example pathway (Phagosome)
|
| 1931 |
+
cat('\n=== Checking Phagosome pathway ===\n')
|
| 1932 |
+
phago <- output[grep('Phagosome', output$Pathway, ignore.case=TRUE), ]
|
| 1933 |
+
print(phago)
|
| 1934 |
+
|
| 1935 |
+
cat('\n=== First 5 rows of final output ===\n')
|
| 1936 |
+
print(head(output, 5))
|
| 1937 |
+
|
| 1938 |
+
cat('\n=== Shared significant pathways ===\n')
|
| 1939 |
+
shared <- output[output$`5xFAD_pvalue` < 0.05 & output$`3xTg_AD_pvalue` < 0.05 & output$PS3O1S_pvalue < 0.05, ]
|
| 1940 |
+
cat('Number of shared significant pathways:', nrow(shared), '\n')
|
| 1941 |
+
print(head(shared, 10))
|
| 1942 |
+
</execute>
|
| 1943 |
+
|
| 1944 |
+
================================== Ai Message ==================================
|
| 1945 |
+
|
| 1946 |
+
<observation>Example pathways:
|
| 1947 |
+
[1] "Glycolysis / Gluconeogenesis Mus musculus mmu00010"
|
| 1948 |
+
[2] "Citrate cycle (TCA cycle) Mus musculus mmu00020"
|
| 1949 |
+
[3] "Pentose phosphate pathway Mus musculus mmu00030"
|
| 1950 |
+
[4] "Pentose and glucuronate interconversions Mus musculus mmu00040"
|
| 1951 |
+
[5] "Fructose and mannose metabolism Mus musculus mmu00051"
|
| 1952 |
+
|
| 1953 |
+
Final output written to pathway_comparison.csv
|
| 1954 |
+
Number of rows: 354
|
| 1955 |
+
|
| 1956 |
+
=== Checking Phagosome pathway ===
|
| 1957 |
+
Pathway 5xFAD_pvalue
|
| 1958 |
+
158 Phagosome Mus musculus mmu04145 1.468729e-45
|
| 1959 |
+
198 Fc gamma R-mediated phagosome formation Mus musculus mmu04666 1.448355e-21
|
| 1960 |
+
3xTg_AD_pvalue PS3O1S_pvalue
|
| 1961 |
+
158 0.044365927 0.0834703935
|
| 1962 |
+
198 0.008033994 0.0000167891
|
| 1963 |
+
|
| 1964 |
+
=== First 5 rows of final output ===
|
| 1965 |
+
Pathway 5xFAD_pvalue
|
| 1966 |
+
1 Glycolysis / Gluconeogenesis Mus musculus mmu00010 0.001888763
|
| 1967 |
+
2 Citrate cycle (TCA cycle) Mus musculus mmu00020 1.000000000
|
| 1968 |
+
3 Pentose phosphate pathway Mus musculus mmu00030 1.000000000
|
| 1969 |
+
4 Pentose and glucuronate interconversions Mus musculus mmu00040 0.002991202
|
| 1970 |
+
5 Fructose and mannose metabolism Mus musculus mmu00051 0.002991202
|
| 1971 |
+
3xTg_AD_pvalue PS3O1S_pvalue
|
| 1972 |
+
1 0.2518787 0.3154502
|
| 1973 |
+
2 1.0000000 0.1655510
|
| 1974 |
+
3 1.0000000 0.1749381
|
| 1975 |
+
4 1.0000000 0.1888214
|
| 1976 |
+
5 1.0000000 1.0000000
|
| 1977 |
+
|
| 1978 |
+
=== Shared significant pathways ===
|
| 1979 |
+
Number of shared significant pathways: 72
|
| 1980 |
+
Pathway 5xFAD_pvalue
|
| 1981 |
+
9 Pyruvate metabolism Mus musculus mmu00620 4.609886e-02
|
| 1982 |
+
25 Glycerophospholipid metabolism Mus musculus mmu00564 1.258381e-03
|
| 1983 |
+
26 Ether lipid metabolism Mus musculus mmu00565 4.040060e-05
|
| 1984 |
+
27 Sphingolipid metabolism Mus musculus mmu00600 2.797931e-07
|
| 1985 |
+
98 Ubiquitin mediated proteolysis Mus musculus mmu04120 7.754758e-03
|
| 1986 |
+
111 Viral life cycle - HIV-1 Mus musculus mmu03250 6.367371e-07
|
| 1987 |
+
121 MAPK signaling pathway Mus musculus mmu04010 3.833075e-17
|
| 1988 |
+
123 Ras signaling pathway Mus musculus mmu04014 6.047823e-08
|
| 1989 |
+
124 Rap1 signaling pathway Mus musculus mmu04015 1.460787e-13
|
| 1990 |
+
125 Wnt signaling pathway Mus musculus mmu04310 1.702020e-06
|
| 1991 |
+
3xTg_AD_pvalue PS3O1S_pvalue
|
| 1992 |
+
9 1.563373e-02 0.0256913162
|
| 1993 |
+
25 8.703075e-05 0.0000267290
|
| 1994 |
+
26 1.274059e-03 0.0313558795
|
| 1995 |
+
27 1.058106e-04 0.0400210384
|
| 1996 |
+
98 3.061695e-02 0.0000330645
|
| 1997 |
+
111 1.675570e-04 0.0494725664
|
| 1998 |
+
121 3.605263e-04 0.0074153766
|
| 1999 |
+
123 3.884875e-03 0.0115315931
|
| 2000 |
+
124 1.437237e-02 0.0002371792
|
| 2001 |
+
125 1.153248e-03 0.0191196942
|
| 2002 |
+
</observation>
|
| 2003 |
+
|
| 2004 |
+
================================== Ai Message ==================================
|
| 2005 |
+
|
| 2006 |
+
<execute>
|
| 2007 |
+
#!BASH
|
| 2008 |
+
echo "=== Verifying the final output file ==="
|
| 2009 |
+
ls -la /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv
|
| 2010 |
+
|
| 2011 |
+
echo ""
|
| 2012 |
+
echo "=== File headers ==="
|
| 2013 |
+
csvtk_headers --tabs false \
|
| 2014 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv
|
| 2015 |
+
|
| 2016 |
+
echo ""
|
| 2017 |
+
echo "=== File dimensions ==="
|
| 2018 |
+
csvtk_dim --tabs false \
|
| 2019 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv
|
| 2020 |
+
|
| 2021 |
+
echo ""
|
| 2022 |
+
echo "=== First 5 rows ==="
|
| 2023 |
+
csvtk_head -n 5 \
|
| 2024 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv
|
| 2025 |
+
|
| 2026 |
+
echo ""
|
| 2027 |
+
echo "=== Checking Phagosome pathway (using grep via csvtk) ==="
|
| 2028 |
+
csvtk_grep -f Pathway -p "Phagosome" \
|
| 2029 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv
|
| 2030 |
+
</execute>
|
| 2031 |
+
|
| 2032 |
+
================================== Ai Message ==================================
|
| 2033 |
+
|
| 2034 |
+
<observation>Error running Bash script (exit code 127):
|
| 2035 |
+
/tmp/tmpgynql4td.sh: line 9: csvtk_headers: command not found
|
| 2036 |
+
</observation>
|
| 2037 |
+
|
| 2038 |
+
================================== Ai Message ==================================
|
| 2039 |
+
|
| 2040 |
+
<execute>
|
| 2041 |
+
#!BASH
|
| 2042 |
+
echo "=== Verifying the final output file ==="
|
| 2043 |
+
ls -la /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv
|
| 2044 |
+
|
| 2045 |
+
echo ""
|
| 2046 |
+
echo "=== First 5 rows ==="
|
| 2047 |
+
head -6 /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv
|
| 2048 |
+
|
| 2049 |
+
echo ""
|
| 2050 |
+
echo "=== Checking for Phagosome ==="
|
| 2051 |
+
grep -i "Phagosome" /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv
|
| 2052 |
+
|
| 2053 |
+
echo ""
|
| 2054 |
+
echo "=== Number of lines ==="
|
| 2055 |
+
wc -l /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv
|
| 2056 |
+
</execute>
|
| 2057 |
+
|
| 2058 |
+
================================== Ai Message ==================================
|
| 2059 |
+
|
| 2060 |
+
<observation>=== Verifying the final output file ===
|
| 2061 |
+
-rw-r--r-- 1 root root 35447 May 15 13:57 /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv
|
| 2062 |
+
|
| 2063 |
+
=== First 5 rows ===
|
| 2064 |
+
"Pathway","5xFAD_pvalue","3xTg_AD_pvalue","PS3O1S_pvalue"
|
| 2065 |
+
"Glycolysis / Gluconeogenesis Mus musculus mmu00010",0.00188876251605204,0.251878661500182,0.315450159417662
|
| 2066 |
+
"Citrate cycle (TCA cycle) Mus musculus mmu00020",1,1,0.165551013512596
|
| 2067 |
+
"Pentose phosphate pathway Mus musculus mmu00030",1,1,0.174938100665575
|
| 2068 |
+
"Pentose and glucuronate interconversions Mus musculus mmu00040",0.00299120206788306,1,0.188821411601279
|
| 2069 |
+
"Fructose and mannose metabolism Mus musculus mmu00051",0.00299120206788306,1,1
|
| 2070 |
+
|
| 2071 |
+
=== Checking for Phagosome ===
|
| 2072 |
+
"Phagosome Mus musculus mmu04145",1.46872870241409e-45,0.0443659270572737,0.0834703935301171
|
| 2073 |
+
"Fc gamma R-mediated phagosome formation Mus musculus mmu04666",1.44835459081155e-21,0.00803399398699419,1.67891012402318e-05
|
| 2074 |
+
|
| 2075 |
+
=== Number of lines ===
|
| 2076 |
+
355 /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv
|
| 2077 |
+
</observation>
|
| 2078 |
+
|
| 2079 |
+
================================== Ai Message ==================================
|
| 2080 |
+
|
| 2081 |
+
Everything looks correct. The output file has been generated successfully. Let me provide the final summary.
|
| 2082 |
+
|
| 2083 |
+
**Final Plan Status:**
|
| 2084 |
+
1. [✓] Examined all input data files (5xFAD counts, 3xTg-AD counts, PS3O1S DEA)
|
| 2085 |
+
2. [✓] Ran DESeq2 for 5xFAD model - found 882 DE genes
|
| 2086 |
+
3. [✓] Ran DESeq2 for 3xTg-AD model - found 578 DE genes
|
| 2087 |
+
4. [✓] Used pre-computed DEA for PS3O1S - 797 significant genes (p<0.05)
|
| 2088 |
+
5. [✓] Mapped Ensembl IDs to Entrez IDs for all three models
|
| 2089 |
+
6. [✓] Performed hypergeometric KEGG pathway enrichment for all three models using KEGGREST
|
| 2090 |
+
7. [✓] Generated final CSV with shared pathway comparison
|
| 2091 |
+
|
| 2092 |
+
The solution file is saved at:
|
| 2093 |
+
`/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv`
|
| 2094 |
+
|
| 2095 |
+
**Summary:**
|
| 2096 |
+
- **354 KEGG pathways** tested across all three Alzheimer's mouse models
|
| 2097 |
+
- **72 pathways** are shared and significantly enriched (p<0.05) across all three models (5xFAD, 3xTg-AD, PS3O1S)
|
| 2098 |
+
- The output CSV contains the required columns: `Pathway`, `5xFAD_pvalue`, `3xTg_AD_pvalue`, `PS3O1S_pvalue`
|
| 2099 |
+
- Each pathway is formatted as: "PathwayName Mus musculus mmuXXXXX" (matching the requested format)
|
| 2100 |
+
|
| 2101 |
+
<solution>
|
| 2102 |
+
The task has been completed. The final output file `pathway_comparison.csv` has been written to:
|
| 2103 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv
|
| 2104 |
+
|
| 2105 |
+
The file contains 354 KEGG pathways with their p-values for all three Alzheimer's mouse models (5xFAD, 3xTg-AD, PS3O1S), with 72 pathways showing significant enrichment (p<0.05) across all three models.
|
| 2106 |
+
</solution>
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/final_answer.txt
ADDED
|
@@ -0,0 +1,26 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
Everything looks correct. The output file has been generated successfully. Let me provide the final summary.
|
| 2 |
+
|
| 3 |
+
**Final Plan Status:**
|
| 4 |
+
1. [✓] Examined all input data files (5xFAD counts, 3xTg-AD counts, PS3O1S DEA)
|
| 5 |
+
2. [✓] Ran DESeq2 for 5xFAD model - found 882 DE genes
|
| 6 |
+
3. [✓] Ran DESeq2 for 3xTg-AD model - found 578 DE genes
|
| 7 |
+
4. [✓] Used pre-computed DEA for PS3O1S - 797 significant genes (p<0.05)
|
| 8 |
+
5. [✓] Mapped Ensembl IDs to Entrez IDs for all three models
|
| 9 |
+
6. [✓] Performed hypergeometric KEGG pathway enrichment for all three models using KEGGREST
|
| 10 |
+
7. [✓] Generated final CSV with shared pathway comparison
|
| 11 |
+
|
| 12 |
+
The solution file is saved at:
|
| 13 |
+
`/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv`
|
| 14 |
+
|
| 15 |
+
**Summary:**
|
| 16 |
+
- **354 KEGG pathways** tested across all three Alzheimer's mouse models
|
| 17 |
+
- **72 pathways** are shared and significantly enriched (p<0.05) across all three models (5xFAD, 3xTg-AD, PS3O1S)
|
| 18 |
+
- The output CSV contains the required columns: `Pathway`, `5xFAD_pvalue`, `3xTg_AD_pvalue`, `PS3O1S_pvalue`
|
| 19 |
+
- Each pathway is formatted as: "PathwayName Mus musculus mmuXXXXX" (matching the requested format)
|
| 20 |
+
|
| 21 |
+
<solution>
|
| 22 |
+
The task has been completed. The final output file `pathway_comparison.csv` has been written to:
|
| 23 |
+
/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv
|
| 24 |
+
|
| 25 |
+
The file contains 354 KEGG pathways with their p-values for all three Alzheimer's mouse models (5xFAD, 3xTg-AD, PS3O1S), with 72 pathways showing significant enrichment (p<0.05) across all three models.
|
| 26 |
+
</solution>
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/kegg_all_pathways.csv
ADDED
|
@@ -0,0 +1,355 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
| 1 |
+
"pathway_id","pathway_name","pval_5xFAD","pval_3xTgAD","pval_PS3O1S"
|
| 2 |
+
"mmu00010","Glycolysis / Gluconeogenesis - Mus musculus (house mouse)",0.00188876251605204,0.251878661500182,0.315450159417662
|
| 3 |
+
"mmu00020","Citrate cycle (TCA cycle) - Mus musculus (house mouse)",1,1,0.165551013512596
|
| 4 |
+
"mmu00030","Pentose phosphate pathway - Mus musculus (house mouse)",1,1,0.174938100665575
|
| 5 |
+
"mmu00040","Pentose and glucuronate interconversions - Mus musculus (house mouse)",0.00299120206788306,1,0.188821411601279
|
| 6 |
+
"mmu00051","Fructose and mannose metabolism - Mus musculus (house mouse)",0.00299120206788306,1,1
|
| 7 |
+
"mmu00052","Galactose metabolism - Mus musculus (house mouse)",0.000109854665750523,1,0.165551013512596
|
| 8 |
+
"mmu00053","Ascorbate and aldarate metabolism - Mus musculus (house mouse)",0.025684979752227,0.129403434832669,1
|
| 9 |
+
"mmu00500","Starch and sucrose metabolism - Mus musculus (house mouse)",0.030345520925155,1,1
|
| 10 |
+
"mmu00620","Pyruvate metabolism - Mus musculus (house mouse)",0.0460988636593801,0.0156337321740566,0.025691316159277
|
| 11 |
+
"mmu00630","Glyoxylate and dicarboxylate metabolism - Mus musculus (house mouse)",0.227158438457303,1,0.0149334993862318
|
| 12 |
+
"mmu00640","Propanoate metabolism - Mus musculus (house mouse)",0.214992500917063,1,0.160817558826275
|
| 13 |
+
"mmu00650","Butanoate metabolism - Mus musculus (house mouse)",1,1,0.141614138865123
|
| 14 |
+
"mmu00660","C5-Branched dibasic acid metabolism - Mus musculus (house mouse)",1,1,1
|
| 15 |
+
"mmu00562","Inositol phosphate metabolism - Mus musculus (house mouse)",3.22496312854122e-05,0.283600242238792,0.0704437059846281
|
| 16 |
+
"mmu00190","Oxidative phosphorylation - Mus musculus (house mouse)",0.299867249046181,1,0.0461255742694992
|
| 17 |
+
"mmu00910","Nitrogen metabolism - Mus musculus (house mouse)",0.124303203486634,1,0.0916641871504653
|
| 18 |
+
"mmu00920","Sulfur metabolism - Mus musculus (house mouse)",1,1,1
|
| 19 |
+
"mmu00061","Fatty acid biosynthesis - Mus musculus (house mouse)",1,1,1
|
| 20 |
+
"mmu00062","Fatty acid elongation - Mus musculus (house mouse)",8.4759418285457e-05,1,1
|
| 21 |
+
"mmu00071","Fatty acid degradation - Mus musculus (house mouse)",1,0.201649119522741,0.254816471519121
|
| 22 |
+
"mmu00100","Steroid biosynthesis - Mus musculus (house mouse)",0.0104608055904814,1,1
|
| 23 |
+
"mmu00120","Primary bile acid biosynthesis - Mus musculus (house mouse)",0.000350566070451028,1,0.0967870661434326
|
| 24 |
+
"mmu00140","Steroid hormone biosynthesis - Mus musculus (house mouse)",0.545655999697596,0.354362566716754,0.435269060902385
|
| 25 |
+
"mmu00561","Glycerolipid metabolism - Mus musculus (house mouse)",0.0865267845010755,0.0305916912749933,1
|
| 26 |
+
"mmu00564","Glycerophospholipid metabolism - Mus musculus (house mouse)",0.00125838146433952,8.7030745355055e-05,2.67290030027644e-05
|
| 27 |
+
"mmu00565","Ether lipid metabolism - Mus musculus (house mouse)",4.0400600083292e-05,0.00127405878492342,0.0313558795397303
|
| 28 |
+
"mmu00600","Sphingolipid metabolism - Mus musculus (house mouse)",2.79793134646224e-07,0.000105810602665975,0.0400210383613077
|
| 29 |
+
"mmu00590","Arachidonic acid metabolism - Mus musculus (house mouse)",7.30481679300735e-05,1.36630247061306e-07,0.395581875081929
|
| 30 |
+
"mmu00591","Linoleic acid metabolism - Mus musculus (house mouse)",1,9.85882784999174e-05,0.267357669902869
|
| 31 |
+
"mmu00592","alpha-Linolenic acid metabolism - Mus musculus (house mouse)",1,0.000171757840949173,0.00874040284972734
|
| 32 |
+
"mmu01040","Biosynthesis of unsaturated fatty acids - Mus musculus (house mouse)",0.000139937983066115,0.136912279662367,0.174938100665575
|
| 33 |
+
"mmu00230","Purine metabolism - Mus musculus (house mouse)",0.00411981627215259,0.00283971781100272,0.175053395947469
|
| 34 |
+
"mmu00240","Pyrimidine metabolism - Mus musculus (house mouse)",0.0728584149211623,0.218755499342715,0.275601173517463
|
| 35 |
+
"mmu00250","Alanine, aspartate and glutamate metabolism - Mus musculus (house mouse)",0.0370331198697317,0.155402844360383,0.197947125157709
|
| 36 |
+
"mmu00260","Glycine, serine and threonine metabolism - Mus musculus (house mouse)",1,0.159053244222123,0.0214976369321462
|
| 37 |
+
"mmu00270","Cysteine and methionine metabolism - Mus musculus (house mouse)",0.359261283048175,1,0.275601173517463
|
| 38 |
+
"mmu00280","Valine, leucine and isoleucine degradation - Mus musculus (house mouse)",0.359261283048175,0.025425231418027,0.275601173517463
|
| 39 |
+
"mmu00290","Valine, leucine and isoleucine biosynthesis - Mus musculus (house mouse)",1,1,1
|
| 40 |
+
"mmu00310","Lysine degradation - Mus musculus (house mouse)",1,0.0314899210731309,0.30373092927997
|
| 41 |
+
"mmu00220","Arginine biosynthesis - Mus musculus (house mouse)",0.151232647719649,1,1
|
| 42 |
+
"mmu00330","Arginine and proline metabolism - Mus musculus (house mouse)",0.344069068853232,0.0229902239137068,1
|
| 43 |
+
"mmu00340","Histidine metabolism - Mus musculus (house mouse)",0.183734173131701,0.106483490694125,1
|
| 44 |
+
"mmu00350","Tyrosine metabolism - Mus musculus (house mouse)",0.0387854714145073,1,1
|
| 45 |
+
"mmu00360","Phenylalanine metabolism - Mus musculus (house mouse)",0.0115028332481941,1,1
|
| 46 |
+
"mmu00380","Tryptophan metabolism - Mus musculus (house mouse)",0.0620675484891288,0.201649119522741,0.034968295275717
|
| 47 |
+
"mmu00400","Phenylalanine, tyrosine and tryptophan biosynthesis - Mus musculus (house mouse)",0.0678571027404098,1,1
|
| 48 |
+
"mmu00410","beta-Alanine metabolism - Mus musculus (house mouse)",0.221099195148187,0.129403434832669,1
|
| 49 |
+
"mmu00430","Taurine and hypotaurine metabolism - Mus musculus (house mouse)",1,0.090869977262429,1
|
| 50 |
+
"mmu00440","Phosphonate and phosphinate metabolism - Mus musculus (house mouse)",1,1,1
|
| 51 |
+
"mmu00450","Selenocompound metabolism - Mus musculus (house mouse)",1,1,0.000114410026166458
|
| 52 |
+
"mmu00470","D-Amino acid metabolism - Mus musculus (house mouse)",0.0457651591471256,1,1
|
| 53 |
+
"mmu00480","Glutathione metabolism - Mus musculus (house mouse)",0.0194942232933578,0.271075954549072,0.338301087870911
|
| 54 |
+
"mmu00520","Amino sugar and nucleotide sugar metabolism - Mus musculus (house mouse)",2.08108743732951e-08,1,0.197947125157709
|
| 55 |
+
"mmu00541","Biosynthesis of various nucleotide sugars - Mus musculus (house mouse)",0.0115028332481941,1,0.00620996651537523
|
| 56 |
+
"mmu00510","N-Glycan biosynthesis - Mus musculus (house mouse)",0.0728584149211623,1,0.0413248856286418
|
| 57 |
+
"mmu00513","Various types of N-glycan biosynthesis - Mus musculus (house mouse)",0.000457344589859219,1,0.229087420628193
|
| 58 |
+
"mmu00512","Mucin type O-glycan biosynthesis - Mus musculus (house mouse)",0.025684979752227,0.129403434832669,0.0140804635503338
|
| 59 |
+
"mmu00515","Mannose type O-glycan biosynthesis - Mus musculus (house mouse)",0.0137169795605896,1,0.00742607040774367
|
| 60 |
+
"mmu00514","Other types of O-glycan biosynthesis - Mus musculus (house mouse)",0.00521736220439448,0.177070421713035,5.69086529972916e-06
|
| 61 |
+
"mmu00532","Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate - Mus musculus (house mouse)",0.151232647719649,1,0.111983269597277
|
| 62 |
+
"mmu00534","Glycosaminoglycan biosynthesis - heparan sulfate / heparin - Mus musculus (house mouse)",0.170885469243319,1,0.126924199995487
|
| 63 |
+
"mmu00533","Glycosaminoglycan biosynthesis - keratan sulfate - Mus musculus (house mouse)",0.103547539447809,1,0.0761208332590591
|
| 64 |
+
"mmu00531","Glycosaminoglycan degradation - Mus musculus (house mouse)",1.06840078496637e-08,0.00370491443986696,1
|
| 65 |
+
"mmu00563","Glycosylphosphatidylinositol (GPI)-anchor biosynthesis - Mus musculus (house mouse)",1,1,0.0124406214665916
|
| 66 |
+
"mmu00601","Glycosphingolipid biosynthesis - lacto and neolacto series - Mus musculus (house mouse)",5.52942010746089e-05,0.11034487561601,0.0101506077691403
|
| 67 |
+
"mmu00603","Glycosphingolipid biosynthesis - globo and isoglobo series - Mus musculus (house mouse)",7.97699631918954e-06,1,0.0916641871504653
|
| 68 |
+
"mmu00604","Glycosphingolipid biosynthesis - ganglio series - Mus musculus (house mouse)",0.000198906280696322,1,1
|
| 69 |
+
"mmu00511","Other glycan degradation - Mus musculus (house mouse)",4.96257438618923e-11,0.0749842020388415,0.0967870661434326
|
| 70 |
+
"mmu00730","Thiamine metabolism - Mus musculus (house mouse)",0.110520124961548,0.0628883519340381,0.0813312351883801
|
| 71 |
+
"mmu00740","Riboflavin metabolism - Mus musculus (house mouse)",1,0.0340473253044041,0.0442329490190337
|
| 72 |
+
"mmu00750","Vitamin B6 metabolism - Mus musculus (house mouse)",1,1,1
|
| 73 |
+
"mmu00760","Nicotinate and nicotinamide metabolism - Mus musculus (house mouse)",0.28522069843127,0.169910245449499,0.215892191619799
|
| 74 |
+
"mmu00770","Pantothenate and CoA biosynthesis - Mus musculus (house mouse)",0.151232647719649,1,1
|
| 75 |
+
"mmu00780","Biotin metabolism - Mus musculus (house mouse)",1,1,1
|
| 76 |
+
"mmu00785","Lipoic acid metabolism - Mus musculus (house mouse)",1,1,0.101881098246601
|
| 77 |
+
"mmu00790","Folate biosynthesis - Mus musculus (house mouse)",0.183734173131701,1,0.136745119194901
|
| 78 |
+
"mmu00670","One carbon pool by folate - Mus musculus (house mouse)",0.0336237450118147,0.148054537515583,0.188821411601279
|
| 79 |
+
"mmu00830","Retinol metabolism - Mus musculus (house mouse)",0.188457587362092,0.010034051236639,0.438456444962096
|
| 80 |
+
"mmu00860","Porphyrin metabolism - Mus musculus (house mouse)",3.29187357897652e-05,1,0.233436376698549
|
| 81 |
+
"mmu00130","Ubiquinone and other terpenoid-quinone biosynthesis - Mus musculus (house mouse)",0.0894381575590584,1,0.0020183349607259
|
| 82 |
+
"mmu00900","Terpenoid backbone biosynthesis - Mus musculus (house mouse)",0.164385559175334,1,1
|
| 83 |
+
"mmu00232","Caffeine metabolism - Mus musculus (house mouse)",1,1,1
|
| 84 |
+
"mmu00524","Neomycin, kanamycin and gentamicin biosynthesis - Mus musculus (house mouse)",0.000594809845419337,1,1
|
| 85 |
+
"mmu00980","Metabolism of xenobiotics by cytochrome P450 - Mus musculus (house mouse)",0.0216630705797098,0.043044653570148,1
|
| 86 |
+
"mmu00982","Drug metabolism - cytochrome P450 - Mus musculus (house mouse)",0.0187993502922434,0.00383278444761316,1
|
| 87 |
+
"mmu00983","Drug metabolism - other enzymes - Mus musculus (house mouse)",0.0393360885538001,0.00850960022656983,1
|
| 88 |
+
"mmu03020","RNA polymerase - Mus musculus (house mouse)",1,0.129403434832669,0.165551013512596
|
| 89 |
+
"mmu03022","Basal transcription factors - Mus musculus (house mouse)",1,1,0.220315467793299
|
| 90 |
+
"mmu03040","Spliceosome - Mus musculus (house mouse)",1,0.478805648484449,0.936831916565462
|
| 91 |
+
"mmu03010","Ribosome - Mus musculus (house mouse)",1,0.0550172895886727,0.115985066845105
|
| 92 |
+
"mmu00970","Aminoacyl-tRNA biosynthesis - Mus musculus (house mouse)",1,1,0.9262170726167
|
| 93 |
+
"mmu03013","Nucleocytoplasmic transport - Mus musculus (house mouse)",0.602180160612018,0.0148314950267854,0.0295588486274545
|
| 94 |
+
"mmu03015","mRNA surveillance pathway - Mus musculus (house mouse)",0.194072635631061,0.0748326230720682,0.000325946658289147
|
| 95 |
+
"mmu03008","Ribosome biogenesis in eukaryotes - Mus musculus (house mouse)",1,0.48465956495412,0.579283600001175
|
| 96 |
+
"mmu03060","Protein export - Mus musculus (house mouse)",1,1,0.00173952519554255
|
| 97 |
+
"mmu04141","Protein processing in endoplasmic reticulum - Mus musculus (house mouse)",0.0528602582070287,0.043765974521276,8.39651727606864e-09
|
| 98 |
+
"mmu04130","SNARE interactions in vesicular transport - Mus musculus (house mouse)",0.233170599133351,1,0.174938100665575
|
| 99 |
+
"mmu04120","Ubiquitin mediated proteolysis - Mus musculus (house mouse)",0.00775475819935914,0.0306169546347054,3.30644983292565e-05
|
| 100 |
+
"mmu04122","Sulfur relay system - Mus musculus (house mouse)",1,1,1
|
| 101 |
+
"mmu03050","Proteasome - Mus musculus (house mouse)",0.0518870677282011,1,0.0290354413918801
|
| 102 |
+
"mmu03018","RNA degradation - Mus musculus (house mouse)",1,0.301985159457587,0.080169409785013
|
| 103 |
+
"mmu03030","DNA replication - Mus musculus (house mouse)",0.245055131488073,1,0.0176217905832604
|
| 104 |
+
"mmu03410","Base excision repair - Mus musculus (house mouse)",0.307206638525126,0.184168962078996,0.000147378833822597
|
| 105 |
+
"mmu03420","Nucleotide excision repair - Mus musculus (house mouse)",1,1,0.00437422571366551
|
| 106 |
+
"mmu03430","Mismatch repair - Mus musculus (house mouse)",1,0.0947986968880939,0.000290557706925856
|
| 107 |
+
"mmu03440","Homologous recombination - Mus musculus (house mouse)",1,1,0.211443861354206
|
| 108 |
+
"mmu03450","Non-homologous end-joining - Mus musculus (house mouse)",1,1,0.0708809265091223
|
| 109 |
+
"mmu03460","Fanconi anemia pathway - Mus musculus (house mouse)",1,0.00151369055768737,1.17183009858575e-05
|
| 110 |
+
"mmu03082","ATP-dependent chromatin remodeling - Mus musculus (house mouse)",0.654391444714672,0.0215328395272374,0.179075423330094
|
| 111 |
+
"mmu03083","Polycomb repressive complex - Mus musculus (house mouse)",1,0.316945722187389,0.0016061025990886
|
| 112 |
+
"mmu03250","Viral life cycle - HIV-1 - Mus musculus (house mouse)",6.36737142693039e-07,0.000167557028548175,0.0494725664334714
|
| 113 |
+
"mmu03260","Virion - Human immunodeficiency virus - Mus musculus (house mouse)",0.0751069646434578,0.042376833528693,1
|
| 114 |
+
"mmu03271","Virion - Rotavirus - Mus musculus (house mouse)",1,1,1
|
| 115 |
+
"mmu03264","Virion - Flavivirus and Alphavirus - Mus musculus (house mouse)",1,0.0547368896059395,1
|
| 116 |
+
"mmu03265","Virion - Ebolavirus, Lyssavirus and Morbillivirus - Mus musculus (house mouse)",0.124303203486634,0.0709696639365147,1
|
| 117 |
+
"mmu03273","Virion - Lassa virus and SFTS virus - Mus musculus (house mouse)",0.151232647719649,0.0869242416695978,1
|
| 118 |
+
"mmu03272","Virion - Hepatitis viruses - Mus musculus (house mouse)",2.9075095083546e-06,1,1
|
| 119 |
+
"mmu03266","Virion - Herpesvirus - Mus musculus (house mouse)",0.0751069646434578,1,1
|
| 120 |
+
"mmu03267","Virion - Adenovirus - Mus musculus (house mouse)",0.0307474158485957,1,1
|
| 121 |
+
"mmu02010","ABC transporters - Mus musculus (house mouse)",0.0105322169997459,0.0262592274221586,0.279688131788749
|
| 122 |
+
"mmu04010","MAPK signaling pathway - Mus musculus (house mouse)",3.83307502211441e-17,0.000360526332451508,0.00741537655421076
|
| 123 |
+
"mmu04012","ErbB signaling pathway - Mus musculus (house mouse)",5.28029405929015e-05,0.305003205099179,0.378234668884088
|
| 124 |
+
"mmu04014","Ras signaling pathway - Mus musculus (house mouse)",6.04782288787434e-08,0.00388487499392564,0.0115315930608717
|
| 125 |
+
"mmu04015","Rap1 signaling pathway - Mus musculus (house mouse)",1.4607874941208e-13,0.0143723741263686,0.000237179245694347
|
| 126 |
+
"mmu04310","Wnt signaling pathway - Mus musculus (house mouse)",1.70201953884582e-06,0.00115324762985833,0.0191196941698186
|
| 127 |
+
"mmu04330","Notch signaling pathway - Mus musculus (house mouse)",0.393356936705734,0.242091639159032,0.050882611875482
|
| 128 |
+
"mmu04340","Hedgehog signaling pathway - Mus musculus (house mouse)",0.364246843267244,1,0.279688131788749
|
| 129 |
+
"mmu04350","TGF-beta signaling pathway - Mus musculus (house mouse)",2.68831763113491e-07,0.384420642464184,0.0258661034582719
|
| 130 |
+
"mmu04390","Hippo signaling pathway - Mus musculus (house mouse)",3.74262225305592e-05,0.149480003839583,3.46751452535817e-07
|
| 131 |
+
"mmu04392","Hippo signaling pathway - multiple species - Mus musculus (house mouse)",0.190083747808751,1,0.141614138865123
|
| 132 |
+
"mmu04370","VEGF signaling pathway - Mus musculus (house mouse)",9.16398069926574e-05,0.0262592274221586,0.0426445520541766
|
| 133 |
+
"mmu04371","Apelin signaling pathway - Mus musculus (house mouse)",1.766266202318e-06,0.0232117352625471,0.00125232324673642
|
| 134 |
+
"mmu04630","JAK-STAT signaling pathway - Mus musculus (house mouse)",2.98033133554481e-20,0.169131529895706,0.620056451561917
|
| 135 |
+
"mmu04064","NF-kappa B signaling pathway - Mus musculus (house mouse)",6.3437938470114e-25,0.0114178047335748,0.122577776983599
|
| 136 |
+
"mmu04668","TNF signaling pathway - Mus musculus (house mouse)",1.74308510265409e-15,0.0148314950267854,0.487079203328975
|
| 137 |
+
"mmu04066","HIF-1 signaling pathway - Mus musculus (house mouse)",5.86905056728738e-13,0.397617746682357,0.48416738972325
|
| 138 |
+
"mmu04068","FoxO signaling pathway - Mus musculus (house mouse)",8.95162012738056e-05,0.113240000778719,0.00703824121203174
|
| 139 |
+
"mmu04020","Calcium signaling pathway - Mus musculus (house mouse)",0.000199605303811666,1.79469576317438e-05,0.00347224424994416
|
| 140 |
+
"mmu04070","Phosphatidylinositol signaling system - Mus musculus (house mouse)",0.000111302194273857,0.340219864078342,0.102517578231723
|
| 141 |
+
"mmu04072","Phospholipase D signaling pathway - Mus musculus (house mouse)",1.64890390569897e-11,0.0272416942145751,0.0103883732407557
|
| 142 |
+
"mmu04071","Sphingolipid signaling pathway - Mus musculus (house mouse)",8.05131061558921e-09,0.11044997080599,0.00667797559028275
|
| 143 |
+
"mmu04024","cAMP signaling pathway - Mus musculus (house mouse)",2.49900337124583e-07,2.74558143370425e-11,7.36310490653198e-07
|
| 144 |
+
"mmu04022","cGMP-PKG signaling pathway - Mus musculus (house mouse)",9.49706810359095e-06,0.0391148261296713,0.253129892551332
|
| 145 |
+
"mmu04151","PI3K-Akt signaling pathway - Mus musculus (house mouse)",4.10249328642366e-18,0.00564371005136584,0.00129174693061495
|
| 146 |
+
"mmu04152","AMPK signaling pathway - Mus musculus (house mouse)",0.0177065678235911,0.0180078871158456,0.00599451995233028
|
| 147 |
+
"mmu04150","mTOR signaling pathway - Mus musculus (house mouse)",0.0015722236237465,1,0.0126587609908749
|
| 148 |
+
"mmu04080","Neuroactive ligand-receptor interaction - Mus musculus (house mouse)",6.84278065369855e-11,2.82060009096783e-09,5.15672881349604e-07
|
| 149 |
+
"mmu04082","Neuroactive ligand signaling - Mus musculus (house mouse)",5.87001560921872e-08,8.58430487797774e-11,9.81107023474811e-12
|
| 150 |
+
"mmu04081","Hormone signaling - Mus musculus (house mouse)",1.54378582652796e-06,4.41955299096117e-09,6.60387911884491e-08
|
| 151 |
+
"mmu04060","Cytokine-cytokine receptor interaction - Mus musculus (house mouse)",1.0349735253958e-40,6.57882847215242e-06,0.0068534953991665
|
| 152 |
+
"mmu04061","Viral protein interaction with cytokine and cytokine receptor - Mus musculus (house mouse)",5.78532861991966e-20,3.95994588414777e-06,0.0168412754094551
|
| 153 |
+
"mmu04512","ECM-receptor interaction - Mus musculus (house mouse)",0.000681106818795333,4.54125520616917e-05,0.0902811667399195
|
| 154 |
+
"mmu04514","Cell adhesion molecule (CAM) interaction - Mus musculus (house mouse)",3.16123114483502e-29,0.181430528609776,0.267701789446283
|
| 155 |
+
"mmu04517","IgSF CAM signaling - Mus musculus (house mouse)",2.1555049003338e-20,0.141436713904788,9.84253307353294e-06
|
| 156 |
+
"mmu04518","Integrin signaling - Mus musculus (house mouse)",1.68098981186179e-12,0.00455311116624863,0.00185074524827744
|
| 157 |
+
"mmu04519","Cadherin signaling - Mus musculus (house mouse)",4.23881329867727e-08,2.47314831381109e-06,1.45175636008651e-07
|
| 158 |
+
"mmu04144","Endocytosis - Mus musculus (house mouse)",6.32577568078068e-14,0.0297310013775663,2.56928028938638e-05
|
| 159 |
+
"mmu04145","Phagosome - Mus musculus (house mouse)",1.46872870241409e-45,0.0443659270572737,0.0834703935301171
|
| 160 |
+
"mmu04142","Lysosome biogenesis - Mus musculus (house mouse)",1.0725141316994e-40,1.74491256263613e-05,3.06384304474036e-10
|
| 161 |
+
"mmu04146","Peroxisome - Mus musculus (house mouse)",1,0.313979431068506,0.0868699806467782
|
| 162 |
+
"mmu04140","Autophagy - animal - Mus musculus (house mouse)",9.93757171848935e-08,1,0.00270448733141765
|
| 163 |
+
"mmu04136","Autophagy - other - Mus musculus (house mouse)",0.221099195148187,1,0.165551013512596
|
| 164 |
+
"mmu04137","Mitophagy - animal - Mus musculus (house mouse)",0.0446125128778969,0.00976972865149759,0.111518887129482
|
| 165 |
+
"mmu04148","Efferocytosis - Mus musculus (house mouse)",7.2381546042206e-17,0.15698393587733,4.37203242840502e-05
|
| 166 |
+
"mmu04110","Cell cycle - Mus musculus (house mouse)",0.000249752728994028,0.00498592986217053,0.00207096578561056
|
| 167 |
+
"mmu04114","Oocyte meiosis - Mus musculus (house mouse)",5.46433424550178e-05,0.00208362125468604,0.000701663380654805
|
| 168 |
+
"mmu04210","Apoptosis - Mus musculus (house mouse)",2.2464425312869e-18,0.00299485492966894,0.0422040245896127
|
| 169 |
+
"mmu04215","Apoptosis - multiple species - Mus musculus (house mouse)",0.025684979752227,0.129403434832669,1
|
| 170 |
+
"mmu04216","Ferroptosis - Mus musculus (house mouse)",1.67137857304199e-05,0.162687899225529,0.206970335312238
|
| 171 |
+
"mmu04217","Necroptosis - Mus musculus (house mouse)",5.34165168408202e-15,0.00109721392957095,0.632750933125029
|
| 172 |
+
"mmu04115","p53 signaling pathway - Mus musculus (house mouse)",1.38135922467865e-07,1,1
|
| 173 |
+
"mmu04218","Cellular senescence - Mus musculus (house mouse)",1.52425372270643e-12,0.543581799122684,0.000613316457287935
|
| 174 |
+
"mmu04510","Focal adhesion - Mus musculus (house mouse)",5.00563332920321e-06,0.0118551064317692,0.00603352685117482
|
| 175 |
+
"mmu04520","Adherens junction - Mus musculus (house mouse)",8.78882955614601e-05,0.0604645887090753,0.0154691309793243
|
| 176 |
+
"mmu04530","Tight junction - Mus musculus (house mouse)",1.13395499475864e-08,0.166079453645071,0.000427474069909468
|
| 177 |
+
"mmu04540","Gap junction - Mus musculus (house mouse)",0.000582488324087001,0.000552407275516627,0.385232416534745
|
| 178 |
+
"mmu04550","Signaling pathways regulating pluripotency of stem cells - Mus musculus (house mouse)",0.00495451041581153,0.0232117352625471,0.0453273079732431
|
| 179 |
+
"mmu04814","Motor proteins - Mus musculus (house mouse)",0.00479293357633098,2.81549354305071e-05,0.10226200662684
|
| 180 |
+
"mmu04820","Cytoskeleton in muscle cells - Mus musculus (house mouse)",6.97130462609646e-11,0.000575657685896498,0.0438319374151194
|
| 181 |
+
"mmu04810","Regulation of actin cytoskeleton - Mus musculus (house mouse)",5.21209964914348e-08,0.268302315889163,6.34326748019767e-05
|
| 182 |
+
"mmu04640","Hematopoietic cell lineage - Mus musculus (house mouse)",2.41897079913994e-31,0.0616220031999561,0.409111054821737
|
| 183 |
+
"mmu04610","Complement and coagulation cascades - Mus musculus (house mouse)",4.15963744504173e-23,0.334476597206305,0.0989761477355028
|
| 184 |
+
"mmu04611","Platelet activation - Mus musculus (house mouse)",2.5053234654609e-16,0.00227403551134449,0.159122236355045
|
| 185 |
+
"mmu04613","Neutrophil extracellular trap formation - Mus musculus (house mouse)",8.93498847135921e-21,0.0132859433564812,0.0012887413045722
|
| 186 |
+
"mmu04620","Toll-like receptor signaling pathway - Mus musculus (house mouse)",8.78185748416153e-27,0.00112531871102263,0.002950983621268
|
| 187 |
+
"mmu04621","NOD-like receptor signaling pathway - Mus musculus (house mouse)",1.01220882389961e-36,0.0139312907764744,0.698800397394389
|
| 188 |
+
"mmu04622","RIG-I-like receptor signaling pathway - Mus musculus (house mouse)",6.21997420798449e-09,1,0.0641933412252838
|
| 189 |
+
"mmu04623","Cytosolic DNA-sensing pathway - Mus musculus (house mouse)",1.25748350239878e-16,1,0.0113674752838335
|
| 190 |
+
"mmu04625","C-type lectin receptor signaling pathway - Mus musculus (house mouse)",7.43750072064657e-16,0.384420642464184,0.469358887545955
|
| 191 |
+
"mmu04650","Natural killer cell mediated cytotoxicity - Mus musculus (house mouse)",2.21583126369907e-07,1,1
|
| 192 |
+
"mmu04612","Antigen processing and presentation - Mus musculus (house mouse)",6.88644871256685e-29,0.0536834077365562,0.00147560659700572
|
| 193 |
+
"mmu04660","T cell receptor signaling pathway - Mus musculus (house mouse)",3.7937341775561e-09,0.0981328802698824,0.000676243866509804
|
| 194 |
+
"mmu04658","Th1 and Th2 cell differentiation - Mus musculus (house mouse)",1.09912067378025e-10,0.316945722187389,0.0137416979305425
|
| 195 |
+
"mmu04659","Th17 cell differentiation - Mus musculus (house mouse)",3.88047058736728e-19,0.365458585169886,0.00305436240486259
|
| 196 |
+
"mmu04657","IL-17 signaling pathway - Mus musculus (house mouse)",0.00100506505032114,0.343072922851875,0.104301260776889
|
| 197 |
+
"mmu04662","B cell receptor signaling pathway - Mus musculus (house mouse)",7.67307846569845e-20,0.00514759448454706,0.0752559400948037
|
| 198 |
+
"mmu04664","Fc epsilon RI signaling pathway - Mus musculus (house mouse)",4.30685642247474e-12,0.00299743901340067,0.311565797003708
|
| 199 |
+
"mmu04666","Fc gamma R-mediated phagosome formation - Mus musculus (house mouse)",1.44835459081155e-21,0.00803399398699419,1.67891012402318e-05
|
| 200 |
+
"mmu04670","Leukocyte transendothelial migration - Mus musculus (house mouse)",6.30409529784988e-21,0.402817188332012,0.0301999230938309
|
| 201 |
+
"mmu04672","Intestinal immune network for IgA production - Mus musculus (house mouse)",1.02822968146852e-17,0.169910245449499,0.0246139901992752
|
| 202 |
+
"mmu04062","Chemokine signaling pathway - Mus musculus (house mouse)",1.48109599343286e-29,2.47147531476248e-05,1.9208159563733e-06
|
| 203 |
+
"mmu04911","Insulin secretion - Mus musculus (house mouse)",0.0298046240077111,0.0536834077365562,0.0851793600446299
|
| 204 |
+
"mmu04910","Insulin signaling pathway - Mus musculus (house mouse)",0.00084481138375678,0.454779588583694,0.187160632122924
|
| 205 |
+
"mmu04922","Glucagon signaling pathway - Mus musculus (house mouse)",0.194072635631061,1,0.117014985077513
|
| 206 |
+
"mmu04923","Regulation of lipolysis in adipocytes - Mus musculus (house mouse)",0.0100445850144994,0.218755499342715,0.0413248856286418
|
| 207 |
+
"mmu04920","Adipocytokine signaling pathway - Mus musculus (house mouse)",0.0187993502922434,0.267910890473549,0.00797809815764336
|
| 208 |
+
"mmu03320","PPAR signaling pathway - Mus musculus (house mouse)",0.00526210618692305,0.319899213661981,0.00167426429745366
|
| 209 |
+
"mmu04929","GnRH secretion - Mus musculus (house mouse)",0.013174045004082,0.23880098731394,0.0494725664334714
|
| 210 |
+
"mmu04912","GnRH signaling pathway - Mus musculus (house mouse)",0.000716598179299081,0.000655728131571385,0.0920014007493891
|
| 211 |
+
"mmu04913","Ovarian steroidogenesis - Mus musculus (house mouse)",0.0137435223783979,0.00274656753272926,0.30373092927997
|
| 212 |
+
"mmu04915","Estrogen signaling pathway - Mus musculus (house mouse)",1.2262757042552e-06,0.0207193060218658,0.0406845373906717
|
| 213 |
+
"mmu04914","Progesterone-mediated oocyte maturation - Mus musculus (house mouse)",7.37377230279297e-07,0.0616220031999561,0.0972187101069175
|
| 214 |
+
"mmu04917","Prolactin signaling pathway - Mus musculus (house mouse)",0.000290845896299439,0.27422736309458,1
|
| 215 |
+
"mmu04921","Oxytocin signaling pathway - Mus musculus (house mouse)",0.00138002735499815,0.00465884744175708,0.00190411233360095
|
| 216 |
+
"mmu04926","Relaxin signaling pathway - Mus musculus (house mouse)",1.01455781624122e-06,0.0195313883131455,0.00093153188399305
|
| 217 |
+
"mmu04935","Growth hormone synthesis, secretion and action - Mus musculus (house mouse)",3.90372855888707e-07,0.000166034431079904,0.028925079200595
|
| 218 |
+
"mmu04918","Thyroid hormone synthesis - Mus musculus (house mouse)",0.0202031294147371,0.0410231307269439,0.00860015296986339
|
| 219 |
+
"mmu04919","Thyroid hormone signaling pathway - Mus musculus (house mouse)",5.0610395466755e-06,0.405400089867294,0.147363620402916
|
| 220 |
+
"mmu04928","Parathyroid hormone synthesis, secretion and action - Mus musculus (house mouse)",3.7593007819949e-05,0.00168265309549448,0.000537894270335414
|
| 221 |
+
"mmu04916","Melanogenesis - Mus musculus (house mouse)",0.00790574090501641,0.35155843884651,0.0192748121737392
|
| 222 |
+
"mmu04924","Renin secretion - Mus musculus (house mouse)",2.10703341705051e-06,0.0420292891194018,0.345747545595115
|
| 223 |
+
"mmu04614","Renin-angiotensin system - Mus musculus (house mouse)",0.00276453469771501,0.14435649352406,0.0176217905832604
|
| 224 |
+
"mmu04925","Aldosterone synthesis and secretion - Mus musculus (house mouse)",0.00904886585090578,0.0748326230720682,0.117014985077513
|
| 225 |
+
"mmu04927","Cortisol synthesis and secretion - Mus musculus (house mouse)",0.0187993502922434,0.00383278444761316,0.00797809815764336
|
| 226 |
+
"mmu04260","Cardiac muscle contraction - Mus musculus (house mouse)",0.152618962785417,0.0570384724232693,0.0902811667399195
|
| 227 |
+
"mmu04261","Adrenergic signaling in cardiomyocytes - Mus musculus (house mouse)",3.41814667786781e-05,0.00062332124129125,0.00201420881806829
|
| 228 |
+
"mmu04270","Vascular smooth muscle contraction - Mus musculus (house mouse)",0.00557343638973988,3.55190581759221e-06,0.0485618979283485
|
| 229 |
+
"mmu04970","Salivary secretion - Mus musculus (house mouse)",6.43180615276134e-05,0.0547937187751002,0.388701747184606
|
| 230 |
+
"mmu04971","Gastric acid secretion - Mus musculus (house mouse)",0.00285239194687625,0.0420292891194018,0.345747545595115
|
| 231 |
+
"mmu04972","Pancreatic secretion - Mus musculus (house mouse)",0.0127312239782337,0.392373129638674,0.137709469417001
|
| 232 |
+
"mmu04976","Bile secretion - Mus musculus (house mouse)",0.00120431527974277,0.0711456518220225,0.111518887129482
|
| 233 |
+
"mmu04973","Carbohydrate digestion and absorption - Mus musculus (house mouse)",2.28760923256851e-06,1,1
|
| 234 |
+
"mmu04974","Protein digestion and absorption - Mus musculus (house mouse)",0.0525562055749065,0.0117070586527484,0.457207073441462
|
| 235 |
+
"mmu04975","Fat digestion and absorption - Mus musculus (house mouse)",0.28522069843127,1,1
|
| 236 |
+
"mmu04979","Cholesterol metabolism - Mus musculus (house mouse)",1.44463367075038e-07,0.198183248516892,0.00303938443540925
|
| 237 |
+
"mmu04977","Vitamin digestion and absorption - Mus musculus (house mouse)",0.183734173131701,0.106483490694125,0.136745119194901
|
| 238 |
+
"mmu04981","Folate transport and metabolism - Mus musculus (house mouse)",0.190083747808751,0.11034487561601,1
|
| 239 |
+
"mmu04980","Cobalamin transport and metabolism - Mus musculus (house mouse)",0.124303203486634,1,1
|
| 240 |
+
"mmu04978","Mineral absorption - Mus musculus (house mouse)",4.61477534927178e-10,0.211957286401154,0.038733231472763
|
| 241 |
+
"mmu04962","Vasopressin-regulated water reabsorption - Mus musculus (house mouse)",0.0460988636593801,1,0.025691316159277
|
| 242 |
+
"mmu04960","Aldosterone-regulated sodium reabsorption - Mus musculus (house mouse)",0.00322896412625358,1,0.19339715365869
|
| 243 |
+
"mmu04961","Endocrine and other factor-regulated calcium reabsorption - Mus musculus (house mouse)",0.0818891006482319,0.0288266453097646,0.291811392786502
|
| 244 |
+
"mmu04964","Proximal tubule bicarbonate reclamation - Mus musculus (house mouse)",0.0125884711463088,1,1
|
| 245 |
+
"mmu04966","Collecting duct acid secretion - Mus musculus (house mouse)",0.0186452315283884,1,0.141614138865123
|
| 246 |
+
"mmu04724","Glutamatergic synapse - Mus musculus (house mouse)",3.90372855888707e-07,0.00173633871193393,3.89052619042805e-07
|
| 247 |
+
"mmu04727","GABAergic synapse - Mus musculus (house mouse)",8.26974958778938e-05,0.325768017910504,0.00181656385088605
|
| 248 |
+
"mmu04725","Cholinergic synapse - Mus musculus (house mouse)",0.000284579866656921,0.00157875792727626,0.00409802877013997
|
| 249 |
+
"mmu04728","Dopaminergic synapse - Mus musculus (house mouse)",0.000754672420613755,0.000344977031803026,0.00113753203036611
|
| 250 |
+
"mmu04726","Serotonergic synapse - Mus musculus (house mouse)",0.00452348423074827,3.21434661649852e-05,0.00113753203036611
|
| 251 |
+
"mmu04720","Long-term potentiation - Mus musculus (house mouse)",0.0155349751253038,1,1
|
| 252 |
+
"mmu04730","Long-term depression - Mus musculus (house mouse)",7.61647770922802e-06,0.0279600440076627,0.0453304673714311
|
| 253 |
+
"mmu04723","Retrograde endocannabinoid signaling - Mus musculus (house mouse)",0.00138002735499815,0.143531145202471,0.00190411233360095
|
| 254 |
+
"mmu04721","Synaptic vesicle cycle - Mus musculus (house mouse)",0.120950846147852,0.0440691261116188,0.000978589078033985
|
| 255 |
+
"mmu04722","Neurotrophin signaling pathway - Mus musculus (house mouse)",5.38256943275912e-06,0.00196297820025809,0.0315039474171441
|
| 256 |
+
"mmu04744","Phototransduction - Mus musculus (house mouse)",0.190083747808751,0.11034487561601,1
|
| 257 |
+
"mmu04740","Olfactory transduction - Mus musculus (house mouse)",0.999244891502537,0.429571084630282,0.912580314278133
|
| 258 |
+
"mmu04742","Taste transduction - Mus musculus (house mouse)",0.160771168255147,0.0604645887090753,0.000184227451937188
|
| 259 |
+
"mmu04750","Inflammatory mediator regulation of TRP channels - Mus musculus (house mouse)",9.13904129031525e-06,2.3924014365093e-05,0.0377306349669488
|
| 260 |
+
"mmu04360","Axon guidance - Mus musculus (house mouse)",0.000586866616669949,0.543581799122684,1.01686425986426e-05
|
| 261 |
+
"mmu04380","Osteoclast differentiation - Mus musculus (house mouse)",1.99893356751902e-41,1.99211118158772e-06,0.171046199014956
|
| 262 |
+
"mmu04382","Cornified envelope formation - Mus musculus (house mouse)",1.68560019717473e-06,0.0162246706921076,0.131305500984044
|
| 263 |
+
"mmu04211","Longevity regulating pathway - Mus musculus (house mouse)",0.0334519735067207,0.32283996060955,0.0920014007493891
|
| 264 |
+
"mmu04213","Longevity regulating pathway - multiple species - Mus musculus (house mouse)",0.0120763521355149,0.232176849129534,0.0466962836503805
|
| 265 |
+
"mmu04710","Circadian rhythm - Mus musculus (house mouse)",1,1,0.0158082462235604
|
| 266 |
+
"mmu04713","Circadian entrainment - Mus musculus (house mouse)",0.00115198532630464,0.0699302870067645,0.00256134584997573
|
| 267 |
+
"mmu04714","Thermogenesis - Mus musculus (house mouse)",0.282848047641328,0.0849843883410256,0.000449245147413152
|
| 268 |
+
"mmu05200","Pathways in cancer - Mus musculus (house mouse)",4.9126800166084e-25,1.10264612861248e-06,0.000343836184543039
|
| 269 |
+
"mmu05202","Transcriptional misregulation in cancer - Mus musculus (house mouse)",4.37315085044035e-19,0.244395423809991,0.00839886129866956
|
| 270 |
+
"mmu05206","MicroRNAs in cancer - Mus musculus (house mouse)",2.82558387670522e-07,0.399600684153957,0.267320420883972
|
| 271 |
+
"mmu05205","Proteoglycans in cancer - Mus musculus (house mouse)",2.26986080140727e-17,0.586916251576845,0.000177162329137342
|
| 272 |
+
"mmu05204","Chemical carcinogenesis - DNA adducts - Mus musculus (house mouse)",0.155327303450842,0.0581727353284494,1
|
| 273 |
+
"mmu05207","Chemical carcinogenesis - receptor activation - Mus musculus (house mouse)",0.00238490203980247,0.0184797167875034,0.374511927709835
|
| 274 |
+
"mmu05208","Chemical carcinogenesis - reactive oxygen species - Mus musculus (house mouse)",8.91002206234376e-05,0.000525779394686351,0.0100551237613953
|
| 275 |
+
"mmu05203","Viral carcinogenesis - Mus musculus (house mouse)",1.31612554406654e-17,0.624518441020119,4.97257421258577e-05
|
| 276 |
+
"mmu05230","Central carbon metabolism in cancer - Mus musculus (house mouse)",1.19250353258677e-06,0.258333173304832,0.323153360225491
|
| 277 |
+
"mmu05231","Choline metabolism in cancer - Mus musculus (house mouse)",0.000124731349413376,7.19704514404848e-05,0.01827935837835
|
| 278 |
+
"mmu05235","PD-L1 expression and PD-1 checkpoint pathway in cancer - Mus musculus (house mouse)",5.43666494802191e-12,0.316945722187389,0.088570638384365
|
| 279 |
+
"mmu05210","Colorectal cancer - Mus musculus (house mouse)",0.000646946220432116,0.00670316590081138,0.392151530044378
|
| 280 |
+
"mmu05212","Pancreatic cancer - Mus musculus (house mouse)",2.99329402772158e-05,1,0.068862965835339
|
| 281 |
+
"mmu05225","Hepatocellular carcinoma - Mus musculus (house mouse)",1.67530662834492e-08,0.0408279447487248,0.0177591933977016
|
| 282 |
+
"mmu05226","Gastric cancer - Mus musculus (house mouse)",3.12292653849371e-06,0.0277110019444481,0.0536193355118311
|
| 283 |
+
"mmu05214","Glioma - Mus musculus (house mouse)",0.000309638331347727,1,0.345747545595115
|
| 284 |
+
"mmu05216","Thyroid cancer - Mus musculus (house mouse)",0.250928225556858,0.148054537515583,1
|
| 285 |
+
"mmu05221","Acute myeloid leukemia - Mus musculus (house mouse)",3.19968006868532e-13,1,0.326972444086767
|
| 286 |
+
"mmu05220","Chronic myeloid leukemia - Mus musculus (house mouse)",2.30523466240765e-06,1,0.349439339991912
|
| 287 |
+
"mmu05217","Basal cell carcinoma - Mus musculus (house mouse)",0.388599400689493,0.23880098731394,0.299780174320525
|
| 288 |
+
"mmu05218","Melanoma - Mus musculus (house mouse)",0.0187993502922434,1,1
|
| 289 |
+
"mmu05211","Renal cell carcinoma - Mus musculus (house mouse)",0.103340516497346,0.261539559282879,0.326972444086767
|
| 290 |
+
"mmu05219","Bladder cancer - Mus musculus (house mouse)",0.0405688046157666,1,1
|
| 291 |
+
"mmu05215","Prostate cancer - Mus musculus (house mouse)",0.000201886832217982,0.370935022736477,0.454125954276949
|
| 292 |
+
"mmu05213","Endometrial cancer - Mus musculus (house mouse)",0.0750843505612129,0.0262592274221586,1
|
| 293 |
+
"mmu05224","Breast cancer - Mus musculus (house mouse)",0.000166845542037538,0.133248078812378,0.564744120265574
|
| 294 |
+
"mmu05222","Small cell lung cancer - Mus musculus (house mouse)",0.00637579279321778,0.062786959921977,0.0989761477355028
|
| 295 |
+
"mmu05223","Non-small cell lung cancer - Mus musculus (house mouse)",0.0187993502922434,0.267910890473549,0.334546187231929
|
| 296 |
+
"mmu05166","Human T-cell leukemia virus 1 infection - Mus musculus (house mouse)",2.42577434972929e-30,0.00446655842494568,0.0131490284129182
|
| 297 |
+
"mmu05170","Human immunodeficiency virus 1 infection - Mus musculus (house mouse)",2.1318904930408e-25,0.000686378626282435,1.11221744409193e-05
|
| 298 |
+
"mmu05161","Hepatitis B - Mus musculus (house mouse)",2.20619810947455e-14,0.0347306091345285,0.236501056377566
|
| 299 |
+
"mmu05160","Hepatitis C - Mus musculus (house mouse)",6.20204758854892e-29,0.508662468061968,0.236501056377566
|
| 300 |
+
"mmu05171","Coronavirus disease - Mus musculus (house mouse)",2.81380455624519e-28,0.0580280914614366,0.00312238417828651
|
| 301 |
+
"mmu05164","Influenza A - Mus musculus (house mouse)",6.3600530830445e-48,0.529513670933104,0.0762094072837038
|
| 302 |
+
"mmu05162","Measles - Mus musculus (house mouse)",8.43478480838255e-28,0.024077092771665,0.0469307761468366
|
| 303 |
+
"mmu05168","Herpes simplex virus 1 infection - Mus musculus (house mouse)",4.02161629623131e-52,0.228502039457436,0.0313645569914615
|
| 304 |
+
"mmu05163","Human cytomegalovirus infection - Mus musculus (house mouse)",3.03521599138782e-27,0.0250920064410405,0.000659759566751578
|
| 305 |
+
"mmu05167","Kaposi sarcoma-associated herpesvirus infection - Mus musculus (house mouse)",4.41765202881021e-29,0.00294347882652543,0.037819367872705
|
| 306 |
+
"mmu05169","Epstein-Barr virus infection - Mus musculus (house mouse)",2.49465523722001e-50,0.0174548405740063,0.00970735538352041
|
| 307 |
+
"mmu05165","Human papillomavirus infection - Mus musculus (house mouse)",7.44185528310093e-24,0.00102016306169048,1.1905573282264e-06
|
| 308 |
+
"mmu05132","Salmonella infection - Mus musculus (house mouse)",4.67397013051126e-20,0.0241589948013569,0.414029708046438
|
| 309 |
+
"mmu05135","Yersinia infection - Mus musculus (house mouse)",9.31226490491198e-16,0.117458789677147,0.00760232082148642
|
| 310 |
+
"mmu05133","Pertussis - Mus musculus (house mouse)",2.30877532752948e-23,0.283600242238792,0.0704437059846281
|
| 311 |
+
"mmu05134","Legionellosis - Mus musculus (house mouse)",1.1789950739829e-12,1,0.00458946133633355
|
| 312 |
+
"mmu05150","Staphylococcus aureus infection - Mus musculus (house mouse)",8.91160478889858e-26,0.0195313883131455,1
|
| 313 |
+
"mmu05152","Tuberculosis - Mus musculus (house mouse)",1.15249943793558e-45,0.182977321352344,0.00372395064813506
|
| 314 |
+
"mmu05100","Bacterial invasion of epithelial cells - Mus musculus (house mouse)",0.000349966884572349,1,0.00958521023699727
|
| 315 |
+
"mmu05146","Amoebiasis - Mus musculus (house mouse)",1.37044773646793e-08,0.370935022736477,0.0229908320912245
|
| 316 |
+
"mmu05144","Malaria - Mus musculus (house mouse)",5.00123379199019e-08,0.00299743901340067,0.00627530496196246
|
| 317 |
+
"mmu05145","Toxoplasmosis - Mus musculus (house mouse)",7.76256106160408e-28,0.0120005035320572,0.000404643454268753
|
| 318 |
+
"mmu05140","Leishmaniasis - Mus musculus (house mouse)",8.0893107511776e-37,0.261539559282879,0.000683937397502903
|
| 319 |
+
"mmu05142","Chagas disease - Mus musculus (house mouse)",2.56251491370645e-25,0.359934570652262,0.000311710520596121
|
| 320 |
+
"mmu05143","African trypanosomiasis - Mus musculus (house mouse)",0.00299120206788306,0.000558337215635567,0.188821411601279
|
| 321 |
+
"mmu05310","Asthma - Mus musculus (house mouse)",1.24732377918536e-11,1,1
|
| 322 |
+
"mmu05322","Systemic lupus erythematosus - Mus musculus (house mouse)",8.1461971895933e-14,0.137634343021916,0.010626487476031
|
| 323 |
+
"mmu05323","Rheumatoid arthritis - Mus musculus (house mouse)",9.29334006400665e-29,0.0547937187751002,0.0133279844533338
|
| 324 |
+
"mmu05320","Autoimmune thyroid disease - Mus musculus (house mouse)",7.91632631601138e-16,0.27422736309458,0.342034834328669
|
| 325 |
+
"mmu05321","Inflammatory bowel disease - Mus musculus (house mouse)",5.50105852633415e-17,1,0.0480770538318894
|
| 326 |
+
"mmu05330","Allograft rejection - Mus musculus (house mouse)",1.97455983908221e-17,0.222132626920269,0.0426445520541766
|
| 327 |
+
"mmu05332","Graft-versus-host disease - Mus musculus (house mouse)",4.4599762940906e-19,0.222132626920269,0.279688131788749
|
| 328 |
+
"mmu05340","Primary immunodeficiency - Mus musculus (house mouse)",8.68256924671514e-06,0.14435649352406,1
|
| 329 |
+
"mmu05010","Alzheimer disease - Mus musculus (house mouse)",1.72151584703171e-08,0.0895636880512323,0.00705389755740247
|
| 330 |
+
"mmu05012","Parkinson disease - Mus musculus (house mouse)",0.00602430645769396,0.00132664179184921,0.00102528873671163
|
| 331 |
+
"mmu05014","Amyotrophic lateral sclerosis - Mus musculus (house mouse)",0.0738821653718355,0.220370387521278,0.00031765193361002
|
| 332 |
+
"mmu05016","Huntington disease - Mus musculus (house mouse)",0.0345711933306865,0.149465484318986,0.000410053884325076
|
| 333 |
+
"mmu05017","Spinocerebellar ataxia - Mus musculus (house mouse)",0.299867249046181,1,0.0461255742694992
|
| 334 |
+
"mmu05020","Prion disease - Mus musculus (house mouse)",7.13977538956423e-10,0.693796550806019,0.00482564340860616
|
| 335 |
+
"mmu05022","Pathways of neurodegeneration - multiple diseases - Mus musculus (house mouse)",3.51861595595774e-07,0.0190475850257936,2.38706044331941e-05
|
| 336 |
+
"mmu05030","Cocaine addiction - Mus musculus (house mouse)",0.0538712457717717,2.16672970706294e-06,0.0301867188622145
|
| 337 |
+
"mmu05031","Amphetamine addiction - Mus musculus (house mouse)",0.100886549037588,0.000238261997096888,0.323153360225491
|
| 338 |
+
"mmu05032","Morphine addiction - Mus musculus (house mouse)",9.33349867566859e-05,0.000741694212295779,1.57924334204489e-05
|
| 339 |
+
"mmu05033","Nicotine addiction - Mus musculus (house mouse)",0.0387854714145073,0.159053244222123,0.0214976369321462
|
| 340 |
+
"mmu05034","Alcoholism - Mus musculus (house mouse)",0.0240180458825765,3.85095331359157e-05,2.7653851469775e-05
|
| 341 |
+
"mmu05417","Lipid and atherosclerosis - Mus musculus (house mouse)",2.00148267748099e-25,0.241212395299811,0.00155917620292144
|
| 342 |
+
"mmu05418","Fluid shear stress and atherosclerosis - Mus musculus (house mouse)",7.32981823233414e-14,0.00414631593399731,0.205523764733473
|
| 343 |
+
"mmu05410","Hypertrophic cardiomyopathy - Mus musculus (house mouse)",0.00790574090501641,0.0699302870067645,0.000271814518334427
|
| 344 |
+
"mmu05412","Arrhythmogenic right ventricular cardiomyopathy - Mus musculus (house mouse)",0.144552041430675,0.311000284950191,0.0851793600446299
|
| 345 |
+
"mmu05414","Dilated cardiomyopathy - Mus musculus (house mouse)",0.00131421890755068,0.0103025015642693,0.00285002066115343
|
| 346 |
+
"mmu05415","Diabetic cardiomyopathy - Mus musculus (house mouse)",2.03241237889416e-08,0.239621576699231,0.00152320077995881
|
| 347 |
+
"mmu05416","Viral myocarditis - Mus musculus (house mouse)",3.12454954518457e-20,0.328683440209422,0.0954703335679758
|
| 348 |
+
"mmu04930","Type II diabetes mellitus - Mus musculus (house mouse)",3.65115193842386e-05,0.187695284442053,1
|
| 349 |
+
"mmu04940","Type I diabetes mellitus - Mus musculus (house mouse)",2.95609384368751e-18,0.032398480049453,0.0523069824664406
|
| 350 |
+
"mmu04950","Maturity onset diabetes of the young - Mus musculus (house mouse)",0.190083747808751,0.11034487561601,1
|
| 351 |
+
"mmu04936","Alcoholic liver disease - Mus musculus (house mouse)",7.7700501442954e-12,0.00340780348519291,0.0086070583454657
|
| 352 |
+
"mmu04932","Non-alcoholic fatty liver disease - Mus musculus (house mouse)",0.000302134222922943,0.155477403411605,0.0137615868731135
|
| 353 |
+
"mmu04931","Insulin resistance - Mus musculus (house mouse)",2.6416902701107e-06,0.0823832704917093,0.0036084634732197
|
| 354 |
+
"mmu04933","AGE-RAGE signaling pathway in diabetic complications - Mus musculus (house mouse)",7.34083809331016e-14,1,0.019783574893119
|
| 355 |
+
"mmu04934","Cushing syndrome - Mus musculus (house mouse)",4.46906708943513e-05,0.000738850610984965,0.00237239082116221
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/metadata_3xTgAD.csv
ADDED
|
@@ -0,0 +1,7 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
sample,condition
|
| 2 |
+
G3R1_Cortex_3xTgAD,3xTgAD
|
| 3 |
+
G3R3_Cortex_3xTgAD,3xTgAD
|
| 4 |
+
G3R4_Cortex_3xTgAD,3xTgAD
|
| 5 |
+
G3R10_Cortex_WT,WT
|
| 6 |
+
G3R7_Cortex_WT,WT
|
| 7 |
+
G3R9_Cortex_WT,WT
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/metadata_5xFAD.csv
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
sample,condition
|
| 2 |
+
5xFAD;BL6_cortex_8mon_Female_295,5xFAD
|
| 3 |
+
5xFAD;BL6_cortex_8mon_Female_312,5xFAD
|
| 4 |
+
5xFAD;BL6_cortex_8mon_Female_339,5xFAD
|
| 5 |
+
5xFAD;BL6_cortex_8mon_Female_341,5xFAD
|
| 6 |
+
5xFAD;BL6_cortex_8mon_Female_342,5xFAD
|
| 7 |
+
5xFAD;BL6_cortex_8mon_Male_299,5xFAD
|
| 8 |
+
5xFAD;BL6_cortex_8mon_Male_300,5xFAD
|
| 9 |
+
5xFAD;BL6_cortex_8mon_Male_307,5xFAD
|
| 10 |
+
5xFAD;BL6_cortex_8mon_Male_387,5xFAD
|
| 11 |
+
5xFAD;BL6_cortex_8mon_Male_390,5xFAD
|
| 12 |
+
BL6_cortex_8mon_Female_322,WT
|
| 13 |
+
BL6_cortex_8mon_Female_338,WT
|
| 14 |
+
BL6_cortex_8mon_Female_340,WT
|
| 15 |
+
BL6_cortex_8mon_Female_348,WT
|
| 16 |
+
BL6_cortex_8mon_Female_351,WT
|
| 17 |
+
BL6_cortex_8mon_Male_389,WT
|
| 18 |
+
BL6_cortex_8mon_Male_396,WT
|
| 19 |
+
BL6_cortex_8mon_Male_399,WT
|
| 20 |
+
BL6_cortex_8mon_Male_410,WT
|
| 21 |
+
BL6_cortex_8mon_Male_412,WT
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/output_validation.json
ADDED
|
@@ -0,0 +1,15 @@
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| 1 |
+
{
|
| 2 |
+
"postprocess": [
|
| 3 |
+
{
|
| 4 |
+
"file": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv",
|
| 5 |
+
"actions": []
|
| 6 |
+
}
|
| 7 |
+
],
|
| 8 |
+
"outputs": [
|
| 9 |
+
{
|
| 10 |
+
"path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv",
|
| 11 |
+
"exists": true,
|
| 12 |
+
"size_bytes": 35447
|
| 13 |
+
}
|
| 14 |
+
]
|
| 15 |
+
}
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv
ADDED
|
@@ -0,0 +1,355 @@
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|
|
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|
|
|
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|
|
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|
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|
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|
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|
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|
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|
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|
|
|
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|
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|
|
|
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|
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|
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|
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|
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|
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|
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|
|
|
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|
|
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|
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|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
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|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
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|
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|
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|
|
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|
|
|
|
|
|
|
|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
"Pathway","5xFAD_pvalue","3xTg_AD_pvalue","PS3O1S_pvalue"
|
| 2 |
+
"Glycolysis / Gluconeogenesis Mus musculus mmu00010",0.00188876251605204,0.251878661500182,0.315450159417662
|
| 3 |
+
"Citrate cycle (TCA cycle) Mus musculus mmu00020",1,1,0.165551013512596
|
| 4 |
+
"Pentose phosphate pathway Mus musculus mmu00030",1,1,0.174938100665575
|
| 5 |
+
"Pentose and glucuronate interconversions Mus musculus mmu00040",0.00299120206788306,1,0.188821411601279
|
| 6 |
+
"Fructose and mannose metabolism Mus musculus mmu00051",0.00299120206788306,1,1
|
| 7 |
+
"Galactose metabolism Mus musculus mmu00052",0.000109854665750523,1,0.165551013512596
|
| 8 |
+
"Ascorbate and aldarate metabolism Mus musculus mmu00053",0.025684979752227,0.129403434832669,1
|
| 9 |
+
"Starch and sucrose metabolism Mus musculus mmu00500",0.030345520925155,1,1
|
| 10 |
+
"Pyruvate metabolism Mus musculus mmu00620",0.0460988636593801,0.0156337321740566,0.025691316159277
|
| 11 |
+
"Glyoxylate and dicarboxylate metabolism Mus musculus mmu00630",0.227158438457303,1,0.0149334993862318
|
| 12 |
+
"Propanoate metabolism Mus musculus mmu00640",0.214992500917063,1,0.160817558826275
|
| 13 |
+
"Butanoate metabolism Mus musculus mmu00650",1,1,0.141614138865123
|
| 14 |
+
"C5-Branched dibasic acid metabolism Mus musculus mmu00660",1,1,1
|
| 15 |
+
"Inositol phosphate metabolism Mus musculus mmu00562",3.22496312854122e-05,0.283600242238792,0.0704437059846281
|
| 16 |
+
"Oxidative phosphorylation Mus musculus mmu00190",0.299867249046181,1,0.0461255742694992
|
| 17 |
+
"Nitrogen metabolism Mus musculus mmu00910",0.124303203486634,1,0.0916641871504653
|
| 18 |
+
"Sulfur metabolism Mus musculus mmu00920",1,1,1
|
| 19 |
+
"Fatty acid biosynthesis Mus musculus mmu00061",1,1,1
|
| 20 |
+
"Fatty acid elongation Mus musculus mmu00062",8.4759418285457e-05,1,1
|
| 21 |
+
"Fatty acid degradation Mus musculus mmu00071",1,0.201649119522741,0.254816471519121
|
| 22 |
+
"Steroid biosynthesis Mus musculus mmu00100",0.0104608055904814,1,1
|
| 23 |
+
"Primary bile acid biosynthesis Mus musculus mmu00120",0.000350566070451028,1,0.0967870661434326
|
| 24 |
+
"Steroid hormone biosynthesis Mus musculus mmu00140",0.545655999697596,0.354362566716754,0.435269060902385
|
| 25 |
+
"Glycerolipid metabolism Mus musculus mmu00561",0.0865267845010755,0.0305916912749933,1
|
| 26 |
+
"Glycerophospholipid metabolism Mus musculus mmu00564",0.00125838146433952,8.7030745355055e-05,2.67290030027644e-05
|
| 27 |
+
"Ether lipid metabolism Mus musculus mmu00565",4.0400600083292e-05,0.00127405878492342,0.0313558795397303
|
| 28 |
+
"Sphingolipid metabolism Mus musculus mmu00600",2.79793134646224e-07,0.000105810602665975,0.0400210383613077
|
| 29 |
+
"Arachidonic acid metabolism Mus musculus mmu00590",7.30481679300735e-05,1.36630247061306e-07,0.395581875081929
|
| 30 |
+
"Linoleic acid metabolism Mus musculus mmu00591",1,9.85882784999174e-05,0.267357669902869
|
| 31 |
+
"alpha-Linolenic acid metabolism Mus musculus mmu00592",1,0.000171757840949173,0.00874040284972734
|
| 32 |
+
"Biosynthesis of unsaturated fatty acids Mus musculus mmu01040",0.000139937983066115,0.136912279662367,0.174938100665575
|
| 33 |
+
"Purine metabolism Mus musculus mmu00230",0.00411981627215259,0.00283971781100272,0.175053395947469
|
| 34 |
+
"Pyrimidine metabolism Mus musculus mmu00240",0.0728584149211623,0.218755499342715,0.275601173517463
|
| 35 |
+
"Alanine, aspartate and glutamate metabolism Mus musculus mmu00250",0.0370331198697317,0.155402844360383,0.197947125157709
|
| 36 |
+
"Glycine, serine and threonine metabolism Mus musculus mmu00260",1,0.159053244222123,0.0214976369321462
|
| 37 |
+
"Cysteine and methionine metabolism Mus musculus mmu00270",0.359261283048175,1,0.275601173517463
|
| 38 |
+
"Valine, leucine and isoleucine degradation Mus musculus mmu00280",0.359261283048175,0.025425231418027,0.275601173517463
|
| 39 |
+
"Valine, leucine and isoleucine biosynthesis Mus musculus mmu00290",1,1,1
|
| 40 |
+
"Lysine degradation Mus musculus mmu00310",1,0.0314899210731309,0.30373092927997
|
| 41 |
+
"Arginine biosynthesis Mus musculus mmu00220",0.151232647719649,1,1
|
| 42 |
+
"Arginine and proline metabolism Mus musculus mmu00330",0.344069068853232,0.0229902239137068,1
|
| 43 |
+
"Histidine metabolism Mus musculus mmu00340",0.183734173131701,0.106483490694125,1
|
| 44 |
+
"Tyrosine metabolism Mus musculus mmu00350",0.0387854714145073,1,1
|
| 45 |
+
"Phenylalanine metabolism Mus musculus mmu00360",0.0115028332481941,1,1
|
| 46 |
+
"Tryptophan metabolism Mus musculus mmu00380",0.0620675484891288,0.201649119522741,0.034968295275717
|
| 47 |
+
"Phenylalanine, tyrosine and tryptophan biosynthesis Mus musculus mmu00400",0.0678571027404098,1,1
|
| 48 |
+
"beta-Alanine metabolism Mus musculus mmu00410",0.221099195148187,0.129403434832669,1
|
| 49 |
+
"Taurine and hypotaurine metabolism Mus musculus mmu00430",1,0.090869977262429,1
|
| 50 |
+
"Phosphonate and phosphinate metabolism Mus musculus mmu00440",1,1,1
|
| 51 |
+
"Selenocompound metabolism Mus musculus mmu00450",1,1,0.000114410026166458
|
| 52 |
+
"D-Amino acid metabolism Mus musculus mmu00470",0.0457651591471256,1,1
|
| 53 |
+
"Glutathione metabolism Mus musculus mmu00480",0.0194942232933578,0.271075954549072,0.338301087870911
|
| 54 |
+
"Amino sugar and nucleotide sugar metabolism Mus musculus mmu00520",2.08108743732951e-08,1,0.197947125157709
|
| 55 |
+
"Biosynthesis of various nucleotide sugars Mus musculus mmu00541",0.0115028332481941,1,0.00620996651537523
|
| 56 |
+
"N-Glycan biosynthesis Mus musculus mmu00510",0.0728584149211623,1,0.0413248856286418
|
| 57 |
+
"Various types of N-glycan biosynthesis Mus musculus mmu00513",0.000457344589859219,1,0.229087420628193
|
| 58 |
+
"Mucin type O-glycan biosynthesis Mus musculus mmu00512",0.025684979752227,0.129403434832669,0.0140804635503338
|
| 59 |
+
"Mannose type O-glycan biosynthesis Mus musculus mmu00515",0.0137169795605896,1,0.00742607040774367
|
| 60 |
+
"Other types of O-glycan biosynthesis Mus musculus mmu00514",0.00521736220439448,0.177070421713035,5.69086529972916e-06
|
| 61 |
+
"Glycosaminoglycan biosynthesis - chondroitin sulfate / dermatan sulfate Mus musculus mmu00532",0.151232647719649,1,0.111983269597277
|
| 62 |
+
"Glycosaminoglycan biosynthesis - heparan sulfate / heparin Mus musculus mmu00534",0.170885469243319,1,0.126924199995487
|
| 63 |
+
"Glycosaminoglycan biosynthesis - keratan sulfate Mus musculus mmu00533",0.103547539447809,1,0.0761208332590591
|
| 64 |
+
"Glycosaminoglycan degradation Mus musculus mmu00531",1.06840078496637e-08,0.00370491443986696,1
|
| 65 |
+
"Glycosylphosphatidylinositol (GPI)-anchor biosynthesis Mus musculus mmu00563",1,1,0.0124406214665916
|
| 66 |
+
"Glycosphingolipid biosynthesis - lacto and neolacto series Mus musculus mmu00601",5.52942010746089e-05,0.11034487561601,0.0101506077691403
|
| 67 |
+
"Glycosphingolipid biosynthesis - globo and isoglobo series Mus musculus mmu00603",7.97699631918954e-06,1,0.0916641871504653
|
| 68 |
+
"Glycosphingolipid biosynthesis - ganglio series Mus musculus mmu00604",0.000198906280696322,1,1
|
| 69 |
+
"Other glycan degradation Mus musculus mmu00511",4.96257438618923e-11,0.0749842020388415,0.0967870661434326
|
| 70 |
+
"Thiamine metabolism Mus musculus mmu00730",0.110520124961548,0.0628883519340381,0.0813312351883801
|
| 71 |
+
"Riboflavin metabolism Mus musculus mmu00740",1,0.0340473253044041,0.0442329490190337
|
| 72 |
+
"Vitamin B6 metabolism Mus musculus mmu00750",1,1,1
|
| 73 |
+
"Nicotinate and nicotinamide metabolism Mus musculus mmu00760",0.28522069843127,0.169910245449499,0.215892191619799
|
| 74 |
+
"Pantothenate and CoA biosynthesis Mus musculus mmu00770",0.151232647719649,1,1
|
| 75 |
+
"Biotin metabolism Mus musculus mmu00780",1,1,1
|
| 76 |
+
"Lipoic acid metabolism Mus musculus mmu00785",1,1,0.101881098246601
|
| 77 |
+
"Folate biosynthesis Mus musculus mmu00790",0.183734173131701,1,0.136745119194901
|
| 78 |
+
"One carbon pool by folate Mus musculus mmu00670",0.0336237450118147,0.148054537515583,0.188821411601279
|
| 79 |
+
"Retinol metabolism Mus musculus mmu00830",0.188457587362092,0.010034051236639,0.438456444962096
|
| 80 |
+
"Porphyrin metabolism Mus musculus mmu00860",3.29187357897652e-05,1,0.233436376698549
|
| 81 |
+
"Ubiquinone and other terpenoid-quinone biosynthesis Mus musculus mmu00130",0.0894381575590584,1,0.0020183349607259
|
| 82 |
+
"Terpenoid backbone biosynthesis Mus musculus mmu00900",0.164385559175334,1,1
|
| 83 |
+
"Caffeine metabolism Mus musculus mmu00232",1,1,1
|
| 84 |
+
"Neomycin, kanamycin and gentamicin biosynthesis Mus musculus mmu00524",0.000594809845419337,1,1
|
| 85 |
+
"Metabolism of xenobiotics by cytochrome P450 Mus musculus mmu00980",0.0216630705797098,0.043044653570148,1
|
| 86 |
+
"Drug metabolism - cytochrome P450 Mus musculus mmu00982",0.0187993502922434,0.00383278444761316,1
|
| 87 |
+
"Drug metabolism - other enzymes Mus musculus mmu00983",0.0393360885538001,0.00850960022656983,1
|
| 88 |
+
"RNA polymerase Mus musculus mmu03020",1,0.129403434832669,0.165551013512596
|
| 89 |
+
"Basal transcription factors Mus musculus mmu03022",1,1,0.220315467793299
|
| 90 |
+
"Spliceosome Mus musculus mmu03040",1,0.478805648484449,0.936831916565462
|
| 91 |
+
"Ribosome Mus musculus mmu03010",1,0.0550172895886727,0.115985066845105
|
| 92 |
+
"Aminoacyl-tRNA biosynthesis Mus musculus mmu00970",1,1,0.9262170726167
|
| 93 |
+
"Nucleocytoplasmic transport Mus musculus mmu03013",0.602180160612018,0.0148314950267854,0.0295588486274545
|
| 94 |
+
"mRNA surveillance pathway Mus musculus mmu03015",0.194072635631061,0.0748326230720682,0.000325946658289147
|
| 95 |
+
"Ribosome biogenesis in eukaryotes Mus musculus mmu03008",1,0.48465956495412,0.579283600001175
|
| 96 |
+
"Protein export Mus musculus mmu03060",1,1,0.00173952519554255
|
| 97 |
+
"Protein processing in endoplasmic reticulum Mus musculus mmu04141",0.0528602582070287,0.043765974521276,8.39651727606864e-09
|
| 98 |
+
"SNARE interactions in vesicular transport Mus musculus mmu04130",0.233170599133351,1,0.174938100665575
|
| 99 |
+
"Ubiquitin mediated proteolysis Mus musculus mmu04120",0.00775475819935914,0.0306169546347054,3.30644983292565e-05
|
| 100 |
+
"Sulfur relay system Mus musculus mmu04122",1,1,1
|
| 101 |
+
"Proteasome Mus musculus mmu03050",0.0518870677282011,1,0.0290354413918801
|
| 102 |
+
"RNA degradation Mus musculus mmu03018",1,0.301985159457587,0.080169409785013
|
| 103 |
+
"DNA replication Mus musculus mmu03030",0.245055131488073,1,0.0176217905832604
|
| 104 |
+
"Base excision repair Mus musculus mmu03410",0.307206638525126,0.184168962078996,0.000147378833822597
|
| 105 |
+
"Nucleotide excision repair Mus musculus mmu03420",1,1,0.00437422571366551
|
| 106 |
+
"Mismatch repair Mus musculus mmu03430",1,0.0947986968880939,0.000290557706925856
|
| 107 |
+
"Homologous recombination Mus musculus mmu03440",1,1,0.211443861354206
|
| 108 |
+
"Non-homologous end-joining Mus musculus mmu03450",1,1,0.0708809265091223
|
| 109 |
+
"Fanconi anemia pathway Mus musculus mmu03460",1,0.00151369055768737,1.17183009858575e-05
|
| 110 |
+
"ATP-dependent chromatin remodeling Mus musculus mmu03082",0.654391444714672,0.0215328395272374,0.179075423330094
|
| 111 |
+
"Polycomb repressive complex Mus musculus mmu03083",1,0.316945722187389,0.0016061025990886
|
| 112 |
+
"Viral life cycle - HIV-1 Mus musculus mmu03250",6.36737142693039e-07,0.000167557028548175,0.0494725664334714
|
| 113 |
+
"Virion - Human immunodeficiency virus Mus musculus mmu03260",0.0751069646434578,0.042376833528693,1
|
| 114 |
+
"Virion - Rotavirus Mus musculus mmu03271",1,1,1
|
| 115 |
+
"Virion - Flavivirus and Alphavirus Mus musculus mmu03264",1,0.0547368896059395,1
|
| 116 |
+
"Virion - Ebolavirus, Lyssavirus and Morbillivirus Mus musculus mmu03265",0.124303203486634,0.0709696639365147,1
|
| 117 |
+
"Virion - Lassa virus and SFTS virus Mus musculus mmu03273",0.151232647719649,0.0869242416695978,1
|
| 118 |
+
"Virion - Hepatitis viruses Mus musculus mmu03272",2.9075095083546e-06,1,1
|
| 119 |
+
"Virion - Herpesvirus Mus musculus mmu03266",0.0751069646434578,1,1
|
| 120 |
+
"Virion - Adenovirus Mus musculus mmu03267",0.0307474158485957,1,1
|
| 121 |
+
"ABC transporters Mus musculus mmu02010",0.0105322169997459,0.0262592274221586,0.279688131788749
|
| 122 |
+
"MAPK signaling pathway Mus musculus mmu04010",3.83307502211441e-17,0.000360526332451508,0.00741537655421076
|
| 123 |
+
"ErbB signaling pathway Mus musculus mmu04012",5.28029405929015e-05,0.305003205099179,0.378234668884088
|
| 124 |
+
"Ras signaling pathway Mus musculus mmu04014",6.04782288787434e-08,0.00388487499392564,0.0115315930608717
|
| 125 |
+
"Rap1 signaling pathway Mus musculus mmu04015",1.4607874941208e-13,0.0143723741263686,0.000237179245694347
|
| 126 |
+
"Wnt signaling pathway Mus musculus mmu04310",1.70201953884582e-06,0.00115324762985833,0.0191196941698186
|
| 127 |
+
"Notch signaling pathway Mus musculus mmu04330",0.393356936705734,0.242091639159032,0.050882611875482
|
| 128 |
+
"Hedgehog signaling pathway Mus musculus mmu04340",0.364246843267244,1,0.279688131788749
|
| 129 |
+
"TGF-beta signaling pathway Mus musculus mmu04350",2.68831763113491e-07,0.384420642464184,0.0258661034582719
|
| 130 |
+
"Hippo signaling pathway Mus musculus mmu04390",3.74262225305592e-05,0.149480003839583,3.46751452535817e-07
|
| 131 |
+
"Hippo signaling pathway - multiple species Mus musculus mmu04392",0.190083747808751,1,0.141614138865123
|
| 132 |
+
"VEGF signaling pathway Mus musculus mmu04370",9.16398069926574e-05,0.0262592274221586,0.0426445520541766
|
| 133 |
+
"Apelin signaling pathway Mus musculus mmu04371",1.766266202318e-06,0.0232117352625471,0.00125232324673642
|
| 134 |
+
"JAK-STAT signaling pathway Mus musculus mmu04630",2.98033133554481e-20,0.169131529895706,0.620056451561917
|
| 135 |
+
"NF-kappa B signaling pathway Mus musculus mmu04064",6.3437938470114e-25,0.0114178047335748,0.122577776983599
|
| 136 |
+
"TNF signaling pathway Mus musculus mmu04668",1.74308510265409e-15,0.0148314950267854,0.487079203328975
|
| 137 |
+
"HIF-1 signaling pathway Mus musculus mmu04066",5.86905056728738e-13,0.397617746682357,0.48416738972325
|
| 138 |
+
"FoxO signaling pathway Mus musculus mmu04068",8.95162012738056e-05,0.113240000778719,0.00703824121203174
|
| 139 |
+
"Calcium signaling pathway Mus musculus mmu04020",0.000199605303811666,1.79469576317438e-05,0.00347224424994416
|
| 140 |
+
"Phosphatidylinositol signaling system Mus musculus mmu04070",0.000111302194273857,0.340219864078342,0.102517578231723
|
| 141 |
+
"Phospholipase D signaling pathway Mus musculus mmu04072",1.64890390569897e-11,0.0272416942145751,0.0103883732407557
|
| 142 |
+
"Sphingolipid signaling pathway Mus musculus mmu04071",8.05131061558921e-09,0.11044997080599,0.00667797559028275
|
| 143 |
+
"cAMP signaling pathway Mus musculus mmu04024",2.49900337124583e-07,2.74558143370425e-11,7.36310490653198e-07
|
| 144 |
+
"cGMP-PKG signaling pathway Mus musculus mmu04022",9.49706810359095e-06,0.0391148261296713,0.253129892551332
|
| 145 |
+
"PI3K-Akt signaling pathway Mus musculus mmu04151",4.10249328642366e-18,0.00564371005136584,0.00129174693061495
|
| 146 |
+
"AMPK signaling pathway Mus musculus mmu04152",0.0177065678235911,0.0180078871158456,0.00599451995233028
|
| 147 |
+
"mTOR signaling pathway Mus musculus mmu04150",0.0015722236237465,1,0.0126587609908749
|
| 148 |
+
"Neuroactive ligand-receptor interaction Mus musculus mmu04080",6.84278065369855e-11,2.82060009096783e-09,5.15672881349604e-07
|
| 149 |
+
"Neuroactive ligand signaling Mus musculus mmu04082",5.87001560921872e-08,8.58430487797774e-11,9.81107023474811e-12
|
| 150 |
+
"Hormone signaling Mus musculus mmu04081",1.54378582652796e-06,4.41955299096117e-09,6.60387911884491e-08
|
| 151 |
+
"Cytokine-cytokine receptor interaction Mus musculus mmu04060",1.0349735253958e-40,6.57882847215242e-06,0.0068534953991665
|
| 152 |
+
"Viral protein interaction with cytokine and cytokine receptor Mus musculus mmu04061",5.78532861991966e-20,3.95994588414777e-06,0.0168412754094551
|
| 153 |
+
"ECM-receptor interaction Mus musculus mmu04512",0.000681106818795333,4.54125520616917e-05,0.0902811667399195
|
| 154 |
+
"Cell adhesion molecule (CAM) interaction Mus musculus mmu04514",3.16123114483502e-29,0.181430528609776,0.267701789446283
|
| 155 |
+
"IgSF CAM signaling Mus musculus mmu04517",2.1555049003338e-20,0.141436713904788,9.84253307353294e-06
|
| 156 |
+
"Integrin signaling Mus musculus mmu04518",1.68098981186179e-12,0.00455311116624863,0.00185074524827744
|
| 157 |
+
"Cadherin signaling Mus musculus mmu04519",4.23881329867727e-08,2.47314831381109e-06,1.45175636008651e-07
|
| 158 |
+
"Endocytosis Mus musculus mmu04144",6.32577568078068e-14,0.0297310013775663,2.56928028938638e-05
|
| 159 |
+
"Phagosome Mus musculus mmu04145",1.46872870241409e-45,0.0443659270572737,0.0834703935301171
|
| 160 |
+
"Lysosome biogenesis Mus musculus mmu04142",1.0725141316994e-40,1.74491256263613e-05,3.06384304474036e-10
|
| 161 |
+
"Peroxisome Mus musculus mmu04146",1,0.313979431068506,0.0868699806467782
|
| 162 |
+
"Autophagy - animal Mus musculus mmu04140",9.93757171848935e-08,1,0.00270448733141765
|
| 163 |
+
"Autophagy - other Mus musculus mmu04136",0.221099195148187,1,0.165551013512596
|
| 164 |
+
"Mitophagy - animal Mus musculus mmu04137",0.0446125128778969,0.00976972865149759,0.111518887129482
|
| 165 |
+
"Efferocytosis Mus musculus mmu04148",7.2381546042206e-17,0.15698393587733,4.37203242840502e-05
|
| 166 |
+
"Cell cycle Mus musculus mmu04110",0.000249752728994028,0.00498592986217053,0.00207096578561056
|
| 167 |
+
"Oocyte meiosis Mus musculus mmu04114",5.46433424550178e-05,0.00208362125468604,0.000701663380654805
|
| 168 |
+
"Apoptosis Mus musculus mmu04210",2.2464425312869e-18,0.00299485492966894,0.0422040245896127
|
| 169 |
+
"Apoptosis - multiple species Mus musculus mmu04215",0.025684979752227,0.129403434832669,1
|
| 170 |
+
"Ferroptosis Mus musculus mmu04216",1.67137857304199e-05,0.162687899225529,0.206970335312238
|
| 171 |
+
"Necroptosis Mus musculus mmu04217",5.34165168408202e-15,0.00109721392957095,0.632750933125029
|
| 172 |
+
"p53 signaling pathway Mus musculus mmu04115",1.38135922467865e-07,1,1
|
| 173 |
+
"Cellular senescence Mus musculus mmu04218",1.52425372270643e-12,0.543581799122684,0.000613316457287935
|
| 174 |
+
"Focal adhesion Mus musculus mmu04510",5.00563332920321e-06,0.0118551064317692,0.00603352685117482
|
| 175 |
+
"Adherens junction Mus musculus mmu04520",8.78882955614601e-05,0.0604645887090753,0.0154691309793243
|
| 176 |
+
"Tight junction Mus musculus mmu04530",1.13395499475864e-08,0.166079453645071,0.000427474069909468
|
| 177 |
+
"Gap junction Mus musculus mmu04540",0.000582488324087001,0.000552407275516627,0.385232416534745
|
| 178 |
+
"Signaling pathways regulating pluripotency of stem cells Mus musculus mmu04550",0.00495451041581153,0.0232117352625471,0.0453273079732431
|
| 179 |
+
"Motor proteins Mus musculus mmu04814",0.00479293357633098,2.81549354305071e-05,0.10226200662684
|
| 180 |
+
"Cytoskeleton in muscle cells Mus musculus mmu04820",6.97130462609646e-11,0.000575657685896498,0.0438319374151194
|
| 181 |
+
"Regulation of actin cytoskeleton Mus musculus mmu04810",5.21209964914348e-08,0.268302315889163,6.34326748019767e-05
|
| 182 |
+
"Hematopoietic cell lineage Mus musculus mmu04640",2.41897079913994e-31,0.0616220031999561,0.409111054821737
|
| 183 |
+
"Complement and coagulation cascades Mus musculus mmu04610",4.15963744504173e-23,0.334476597206305,0.0989761477355028
|
| 184 |
+
"Platelet activation Mus musculus mmu04611",2.5053234654609e-16,0.00227403551134449,0.159122236355045
|
| 185 |
+
"Neutrophil extracellular trap formation Mus musculus mmu04613",8.93498847135921e-21,0.0132859433564812,0.0012887413045722
|
| 186 |
+
"Toll-like receptor signaling pathway Mus musculus mmu04620",8.78185748416153e-27,0.00112531871102263,0.002950983621268
|
| 187 |
+
"NOD-like receptor signaling pathway Mus musculus mmu04621",1.01220882389961e-36,0.0139312907764744,0.698800397394389
|
| 188 |
+
"RIG-I-like receptor signaling pathway Mus musculus mmu04622",6.21997420798449e-09,1,0.0641933412252838
|
| 189 |
+
"Cytosolic DNA-sensing pathway Mus musculus mmu04623",1.25748350239878e-16,1,0.0113674752838335
|
| 190 |
+
"C-type lectin receptor signaling pathway Mus musculus mmu04625",7.43750072064657e-16,0.384420642464184,0.469358887545955
|
| 191 |
+
"Natural killer cell mediated cytotoxicity Mus musculus mmu04650",2.21583126369907e-07,1,1
|
| 192 |
+
"Antigen processing and presentation Mus musculus mmu04612",6.88644871256685e-29,0.0536834077365562,0.00147560659700572
|
| 193 |
+
"T cell receptor signaling pathway Mus musculus mmu04660",3.7937341775561e-09,0.0981328802698824,0.000676243866509804
|
| 194 |
+
"Th1 and Th2 cell differentiation Mus musculus mmu04658",1.09912067378025e-10,0.316945722187389,0.0137416979305425
|
| 195 |
+
"Th17 cell differentiation Mus musculus mmu04659",3.88047058736728e-19,0.365458585169886,0.00305436240486259
|
| 196 |
+
"IL-17 signaling pathway Mus musculus mmu04657",0.00100506505032114,0.343072922851875,0.104301260776889
|
| 197 |
+
"B cell receptor signaling pathway Mus musculus mmu04662",7.67307846569845e-20,0.00514759448454706,0.0752559400948037
|
| 198 |
+
"Fc epsilon RI signaling pathway Mus musculus mmu04664",4.30685642247474e-12,0.00299743901340067,0.311565797003708
|
| 199 |
+
"Fc gamma R-mediated phagosome formation Mus musculus mmu04666",1.44835459081155e-21,0.00803399398699419,1.67891012402318e-05
|
| 200 |
+
"Leukocyte transendothelial migration Mus musculus mmu04670",6.30409529784988e-21,0.402817188332012,0.0301999230938309
|
| 201 |
+
"Intestinal immune network for IgA production Mus musculus mmu04672",1.02822968146852e-17,0.169910245449499,0.0246139901992752
|
| 202 |
+
"Chemokine signaling pathway Mus musculus mmu04062",1.48109599343286e-29,2.47147531476248e-05,1.9208159563733e-06
|
| 203 |
+
"Insulin secretion Mus musculus mmu04911",0.0298046240077111,0.0536834077365562,0.0851793600446299
|
| 204 |
+
"Insulin signaling pathway Mus musculus mmu04910",0.00084481138375678,0.454779588583694,0.187160632122924
|
| 205 |
+
"Glucagon signaling pathway Mus musculus mmu04922",0.194072635631061,1,0.117014985077513
|
| 206 |
+
"Regulation of lipolysis in adipocytes Mus musculus mmu04923",0.0100445850144994,0.218755499342715,0.0413248856286418
|
| 207 |
+
"Adipocytokine signaling pathway Mus musculus mmu04920",0.0187993502922434,0.267910890473549,0.00797809815764336
|
| 208 |
+
"PPAR signaling pathway Mus musculus mmu03320",0.00526210618692305,0.319899213661981,0.00167426429745366
|
| 209 |
+
"GnRH secretion Mus musculus mmu04929",0.013174045004082,0.23880098731394,0.0494725664334714
|
| 210 |
+
"GnRH signaling pathway Mus musculus mmu04912",0.000716598179299081,0.000655728131571385,0.0920014007493891
|
| 211 |
+
"Ovarian steroidogenesis Mus musculus mmu04913",0.0137435223783979,0.00274656753272926,0.30373092927997
|
| 212 |
+
"Estrogen signaling pathway Mus musculus mmu04915",1.2262757042552e-06,0.0207193060218658,0.0406845373906717
|
| 213 |
+
"Progesterone-mediated oocyte maturation Mus musculus mmu04914",7.37377230279297e-07,0.0616220031999561,0.0972187101069175
|
| 214 |
+
"Prolactin signaling pathway Mus musculus mmu04917",0.000290845896299439,0.27422736309458,1
|
| 215 |
+
"Oxytocin signaling pathway Mus musculus mmu04921",0.00138002735499815,0.00465884744175708,0.00190411233360095
|
| 216 |
+
"Relaxin signaling pathway Mus musculus mmu04926",1.01455781624122e-06,0.0195313883131455,0.00093153188399305
|
| 217 |
+
"Growth hormone synthesis, secretion and action Mus musculus mmu04935",3.90372855888707e-07,0.000166034431079904,0.028925079200595
|
| 218 |
+
"Thyroid hormone synthesis Mus musculus mmu04918",0.0202031294147371,0.0410231307269439,0.00860015296986339
|
| 219 |
+
"Thyroid hormone signaling pathway Mus musculus mmu04919",5.0610395466755e-06,0.405400089867294,0.147363620402916
|
| 220 |
+
"Parathyroid hormone synthesis, secretion and action Mus musculus mmu04928",3.7593007819949e-05,0.00168265309549448,0.000537894270335414
|
| 221 |
+
"Melanogenesis Mus musculus mmu04916",0.00790574090501641,0.35155843884651,0.0192748121737392
|
| 222 |
+
"Renin secretion Mus musculus mmu04924",2.10703341705051e-06,0.0420292891194018,0.345747545595115
|
| 223 |
+
"Renin-angiotensin system Mus musculus mmu04614",0.00276453469771501,0.14435649352406,0.0176217905832604
|
| 224 |
+
"Aldosterone synthesis and secretion Mus musculus mmu04925",0.00904886585090578,0.0748326230720682,0.117014985077513
|
| 225 |
+
"Cortisol synthesis and secretion Mus musculus mmu04927",0.0187993502922434,0.00383278444761316,0.00797809815764336
|
| 226 |
+
"Cardiac muscle contraction Mus musculus mmu04260",0.152618962785417,0.0570384724232693,0.0902811667399195
|
| 227 |
+
"Adrenergic signaling in cardiomyocytes Mus musculus mmu04261",3.41814667786781e-05,0.00062332124129125,0.00201420881806829
|
| 228 |
+
"Vascular smooth muscle contraction Mus musculus mmu04270",0.00557343638973988,3.55190581759221e-06,0.0485618979283485
|
| 229 |
+
"Salivary secretion Mus musculus mmu04970",6.43180615276134e-05,0.0547937187751002,0.388701747184606
|
| 230 |
+
"Gastric acid secretion Mus musculus mmu04971",0.00285239194687625,0.0420292891194018,0.345747545595115
|
| 231 |
+
"Pancreatic secretion Mus musculus mmu04972",0.0127312239782337,0.392373129638674,0.137709469417001
|
| 232 |
+
"Bile secretion Mus musculus mmu04976",0.00120431527974277,0.0711456518220225,0.111518887129482
|
| 233 |
+
"Carbohydrate digestion and absorption Mus musculus mmu04973",2.28760923256851e-06,1,1
|
| 234 |
+
"Protein digestion and absorption Mus musculus mmu04974",0.0525562055749065,0.0117070586527484,0.457207073441462
|
| 235 |
+
"Fat digestion and absorption Mus musculus mmu04975",0.28522069843127,1,1
|
| 236 |
+
"Cholesterol metabolism Mus musculus mmu04979",1.44463367075038e-07,0.198183248516892,0.00303938443540925
|
| 237 |
+
"Vitamin digestion and absorption Mus musculus mmu04977",0.183734173131701,0.106483490694125,0.136745119194901
|
| 238 |
+
"Folate transport and metabolism Mus musculus mmu04981",0.190083747808751,0.11034487561601,1
|
| 239 |
+
"Cobalamin transport and metabolism Mus musculus mmu04980",0.124303203486634,1,1
|
| 240 |
+
"Mineral absorption Mus musculus mmu04978",4.61477534927178e-10,0.211957286401154,0.038733231472763
|
| 241 |
+
"Vasopressin-regulated water reabsorption Mus musculus mmu04962",0.0460988636593801,1,0.025691316159277
|
| 242 |
+
"Aldosterone-regulated sodium reabsorption Mus musculus mmu04960",0.00322896412625358,1,0.19339715365869
|
| 243 |
+
"Endocrine and other factor-regulated calcium reabsorption Mus musculus mmu04961",0.0818891006482319,0.0288266453097646,0.291811392786502
|
| 244 |
+
"Proximal tubule bicarbonate reclamation Mus musculus mmu04964",0.0125884711463088,1,1
|
| 245 |
+
"Collecting duct acid secretion Mus musculus mmu04966",0.0186452315283884,1,0.141614138865123
|
| 246 |
+
"Glutamatergic synapse Mus musculus mmu04724",3.90372855888707e-07,0.00173633871193393,3.89052619042805e-07
|
| 247 |
+
"GABAergic synapse Mus musculus mmu04727",8.26974958778938e-05,0.325768017910504,0.00181656385088605
|
| 248 |
+
"Cholinergic synapse Mus musculus mmu04725",0.000284579866656921,0.00157875792727626,0.00409802877013997
|
| 249 |
+
"Dopaminergic synapse Mus musculus mmu04728",0.000754672420613755,0.000344977031803026,0.00113753203036611
|
| 250 |
+
"Serotonergic synapse Mus musculus mmu04726",0.00452348423074827,3.21434661649852e-05,0.00113753203036611
|
| 251 |
+
"Long-term potentiation Mus musculus mmu04720",0.0155349751253038,1,1
|
| 252 |
+
"Long-term depression Mus musculus mmu04730",7.61647770922802e-06,0.0279600440076627,0.0453304673714311
|
| 253 |
+
"Retrograde endocannabinoid signaling Mus musculus mmu04723",0.00138002735499815,0.143531145202471,0.00190411233360095
|
| 254 |
+
"Synaptic vesicle cycle Mus musculus mmu04721",0.120950846147852,0.0440691261116188,0.000978589078033985
|
| 255 |
+
"Neurotrophin signaling pathway Mus musculus mmu04722",5.38256943275912e-06,0.00196297820025809,0.0315039474171441
|
| 256 |
+
"Phototransduction Mus musculus mmu04744",0.190083747808751,0.11034487561601,1
|
| 257 |
+
"Olfactory transduction Mus musculus mmu04740",0.999244891502537,0.429571084630282,0.912580314278133
|
| 258 |
+
"Taste transduction Mus musculus mmu04742",0.160771168255147,0.0604645887090753,0.000184227451937188
|
| 259 |
+
"Inflammatory mediator regulation of TRP channels Mus musculus mmu04750",9.13904129031525e-06,2.3924014365093e-05,0.0377306349669488
|
| 260 |
+
"Axon guidance Mus musculus mmu04360",0.000586866616669949,0.543581799122684,1.01686425986426e-05
|
| 261 |
+
"Osteoclast differentiation Mus musculus mmu04380",1.99893356751902e-41,1.99211118158772e-06,0.171046199014956
|
| 262 |
+
"Cornified envelope formation Mus musculus mmu04382",1.68560019717473e-06,0.0162246706921076,0.131305500984044
|
| 263 |
+
"Longevity regulating pathway Mus musculus mmu04211",0.0334519735067207,0.32283996060955,0.0920014007493891
|
| 264 |
+
"Longevity regulating pathway - multiple species Mus musculus mmu04213",0.0120763521355149,0.232176849129534,0.0466962836503805
|
| 265 |
+
"Circadian rhythm Mus musculus mmu04710",1,1,0.0158082462235604
|
| 266 |
+
"Circadian entrainment Mus musculus mmu04713",0.00115198532630464,0.0699302870067645,0.00256134584997573
|
| 267 |
+
"Thermogenesis Mus musculus mmu04714",0.282848047641328,0.0849843883410256,0.000449245147413152
|
| 268 |
+
"Pathways in cancer Mus musculus mmu05200",4.9126800166084e-25,1.10264612861248e-06,0.000343836184543039
|
| 269 |
+
"Transcriptional misregulation in cancer Mus musculus mmu05202",4.37315085044035e-19,0.244395423809991,0.00839886129866956
|
| 270 |
+
"MicroRNAs in cancer Mus musculus mmu05206",2.82558387670522e-07,0.399600684153957,0.267320420883972
|
| 271 |
+
"Proteoglycans in cancer Mus musculus mmu05205",2.26986080140727e-17,0.586916251576845,0.000177162329137342
|
| 272 |
+
"Chemical carcinogenesis - DNA adducts Mus musculus mmu05204",0.155327303450842,0.0581727353284494,1
|
| 273 |
+
"Chemical carcinogenesis - receptor activation Mus musculus mmu05207",0.00238490203980247,0.0184797167875034,0.374511927709835
|
| 274 |
+
"Chemical carcinogenesis - reactive oxygen species Mus musculus mmu05208",8.91002206234376e-05,0.000525779394686351,0.0100551237613953
|
| 275 |
+
"Viral carcinogenesis Mus musculus mmu05203",1.31612554406654e-17,0.624518441020119,4.97257421258577e-05
|
| 276 |
+
"Central carbon metabolism in cancer Mus musculus mmu05230",1.19250353258677e-06,0.258333173304832,0.323153360225491
|
| 277 |
+
"Choline metabolism in cancer Mus musculus mmu05231",0.000124731349413376,7.19704514404848e-05,0.01827935837835
|
| 278 |
+
"PD-L1 expression and PD-1 checkpoint pathway in cancer Mus musculus mmu05235",5.43666494802191e-12,0.316945722187389,0.088570638384365
|
| 279 |
+
"Colorectal cancer Mus musculus mmu05210",0.000646946220432116,0.00670316590081138,0.392151530044378
|
| 280 |
+
"Pancreatic cancer Mus musculus mmu05212",2.99329402772158e-05,1,0.068862965835339
|
| 281 |
+
"Hepatocellular carcinoma Mus musculus mmu05225",1.67530662834492e-08,0.0408279447487248,0.0177591933977016
|
| 282 |
+
"Gastric cancer Mus musculus mmu05226",3.12292653849371e-06,0.0277110019444481,0.0536193355118311
|
| 283 |
+
"Glioma Mus musculus mmu05214",0.000309638331347727,1,0.345747545595115
|
| 284 |
+
"Thyroid cancer Mus musculus mmu05216",0.250928225556858,0.148054537515583,1
|
| 285 |
+
"Acute myeloid leukemia Mus musculus mmu05221",3.19968006868532e-13,1,0.326972444086767
|
| 286 |
+
"Chronic myeloid leukemia Mus musculus mmu05220",2.30523466240765e-06,1,0.349439339991912
|
| 287 |
+
"Basal cell carcinoma Mus musculus mmu05217",0.388599400689493,0.23880098731394,0.299780174320525
|
| 288 |
+
"Melanoma Mus musculus mmu05218",0.0187993502922434,1,1
|
| 289 |
+
"Renal cell carcinoma Mus musculus mmu05211",0.103340516497346,0.261539559282879,0.326972444086767
|
| 290 |
+
"Bladder cancer Mus musculus mmu05219",0.0405688046157666,1,1
|
| 291 |
+
"Prostate cancer Mus musculus mmu05215",0.000201886832217982,0.370935022736477,0.454125954276949
|
| 292 |
+
"Endometrial cancer Mus musculus mmu05213",0.0750843505612129,0.0262592274221586,1
|
| 293 |
+
"Breast cancer Mus musculus mmu05224",0.000166845542037538,0.133248078812378,0.564744120265574
|
| 294 |
+
"Small cell lung cancer Mus musculus mmu05222",0.00637579279321778,0.062786959921977,0.0989761477355028
|
| 295 |
+
"Non-small cell lung cancer Mus musculus mmu05223",0.0187993502922434,0.267910890473549,0.334546187231929
|
| 296 |
+
"Human T-cell leukemia virus 1 infection Mus musculus mmu05166",2.42577434972929e-30,0.00446655842494568,0.0131490284129182
|
| 297 |
+
"Human immunodeficiency virus 1 infection Mus musculus mmu05170",2.1318904930408e-25,0.000686378626282435,1.11221744409193e-05
|
| 298 |
+
"Hepatitis B Mus musculus mmu05161",2.20619810947455e-14,0.0347306091345285,0.236501056377566
|
| 299 |
+
"Hepatitis C Mus musculus mmu05160",6.20204758854892e-29,0.508662468061968,0.236501056377566
|
| 300 |
+
"Coronavirus disease Mus musculus mmu05171",2.81380455624519e-28,0.0580280914614366,0.00312238417828651
|
| 301 |
+
"Influenza A Mus musculus mmu05164",6.3600530830445e-48,0.529513670933104,0.0762094072837038
|
| 302 |
+
"Measles Mus musculus mmu05162",8.43478480838255e-28,0.024077092771665,0.0469307761468366
|
| 303 |
+
"Herpes simplex virus 1 infection Mus musculus mmu05168",4.02161629623131e-52,0.228502039457436,0.0313645569914615
|
| 304 |
+
"Human cytomegalovirus infection Mus musculus mmu05163",3.03521599138782e-27,0.0250920064410405,0.000659759566751578
|
| 305 |
+
"Kaposi sarcoma-associated herpesvirus infection Mus musculus mmu05167",4.41765202881021e-29,0.00294347882652543,0.037819367872705
|
| 306 |
+
"Epstein-Barr virus infection Mus musculus mmu05169",2.49465523722001e-50,0.0174548405740063,0.00970735538352041
|
| 307 |
+
"Human papillomavirus infection Mus musculus mmu05165",7.44185528310093e-24,0.00102016306169048,1.1905573282264e-06
|
| 308 |
+
"Salmonella infection Mus musculus mmu05132",4.67397013051126e-20,0.0241589948013569,0.414029708046438
|
| 309 |
+
"Yersinia infection Mus musculus mmu05135",9.31226490491198e-16,0.117458789677147,0.00760232082148642
|
| 310 |
+
"Pertussis Mus musculus mmu05133",2.30877532752948e-23,0.283600242238792,0.0704437059846281
|
| 311 |
+
"Legionellosis Mus musculus mmu05134",1.1789950739829e-12,1,0.00458946133633355
|
| 312 |
+
"Staphylococcus aureus infection Mus musculus mmu05150",8.91160478889858e-26,0.0195313883131455,1
|
| 313 |
+
"Tuberculosis Mus musculus mmu05152",1.15249943793558e-45,0.182977321352344,0.00372395064813506
|
| 314 |
+
"Bacterial invasion of epithelial cells Mus musculus mmu05100",0.000349966884572349,1,0.00958521023699727
|
| 315 |
+
"Amoebiasis Mus musculus mmu05146",1.37044773646793e-08,0.370935022736477,0.0229908320912245
|
| 316 |
+
"Malaria Mus musculus mmu05144",5.00123379199019e-08,0.00299743901340067,0.00627530496196246
|
| 317 |
+
"Toxoplasmosis Mus musculus mmu05145",7.76256106160408e-28,0.0120005035320572,0.000404643454268753
|
| 318 |
+
"Leishmaniasis Mus musculus mmu05140",8.0893107511776e-37,0.261539559282879,0.000683937397502903
|
| 319 |
+
"Chagas disease Mus musculus mmu05142",2.56251491370645e-25,0.359934570652262,0.000311710520596121
|
| 320 |
+
"African trypanosomiasis Mus musculus mmu05143",0.00299120206788306,0.000558337215635567,0.188821411601279
|
| 321 |
+
"Asthma Mus musculus mmu05310",1.24732377918536e-11,1,1
|
| 322 |
+
"Systemic lupus erythematosus Mus musculus mmu05322",8.1461971895933e-14,0.137634343021916,0.010626487476031
|
| 323 |
+
"Rheumatoid arthritis Mus musculus mmu05323",9.29334006400665e-29,0.0547937187751002,0.0133279844533338
|
| 324 |
+
"Autoimmune thyroid disease Mus musculus mmu05320",7.91632631601138e-16,0.27422736309458,0.342034834328669
|
| 325 |
+
"Inflammatory bowel disease Mus musculus mmu05321",5.50105852633415e-17,1,0.0480770538318894
|
| 326 |
+
"Allograft rejection Mus musculus mmu05330",1.97455983908221e-17,0.222132626920269,0.0426445520541766
|
| 327 |
+
"Graft-versus-host disease Mus musculus mmu05332",4.4599762940906e-19,0.222132626920269,0.279688131788749
|
| 328 |
+
"Primary immunodeficiency Mus musculus mmu05340",8.68256924671514e-06,0.14435649352406,1
|
| 329 |
+
"Alzheimer disease Mus musculus mmu05010",1.72151584703171e-08,0.0895636880512323,0.00705389755740247
|
| 330 |
+
"Parkinson disease Mus musculus mmu05012",0.00602430645769396,0.00132664179184921,0.00102528873671163
|
| 331 |
+
"Amyotrophic lateral sclerosis Mus musculus mmu05014",0.0738821653718355,0.220370387521278,0.00031765193361002
|
| 332 |
+
"Huntington disease Mus musculus mmu05016",0.0345711933306865,0.149465484318986,0.000410053884325076
|
| 333 |
+
"Spinocerebellar ataxia Mus musculus mmu05017",0.299867249046181,1,0.0461255742694992
|
| 334 |
+
"Prion disease Mus musculus mmu05020",7.13977538956423e-10,0.693796550806019,0.00482564340860616
|
| 335 |
+
"Pathways of neurodegeneration - multiple diseases Mus musculus mmu05022",3.51861595595774e-07,0.0190475850257936,2.38706044331941e-05
|
| 336 |
+
"Cocaine addiction Mus musculus mmu05030",0.0538712457717717,2.16672970706294e-06,0.0301867188622145
|
| 337 |
+
"Amphetamine addiction Mus musculus mmu05031",0.100886549037588,0.000238261997096888,0.323153360225491
|
| 338 |
+
"Morphine addiction Mus musculus mmu05032",9.33349867566859e-05,0.000741694212295779,1.57924334204489e-05
|
| 339 |
+
"Nicotine addiction Mus musculus mmu05033",0.0387854714145073,0.159053244222123,0.0214976369321462
|
| 340 |
+
"Alcoholism Mus musculus mmu05034",0.0240180458825765,3.85095331359157e-05,2.7653851469775e-05
|
| 341 |
+
"Lipid and atherosclerosis Mus musculus mmu05417",2.00148267748099e-25,0.241212395299811,0.00155917620292144
|
| 342 |
+
"Fluid shear stress and atherosclerosis Mus musculus mmu05418",7.32981823233414e-14,0.00414631593399731,0.205523764733473
|
| 343 |
+
"Hypertrophic cardiomyopathy Mus musculus mmu05410",0.00790574090501641,0.0699302870067645,0.000271814518334427
|
| 344 |
+
"Arrhythmogenic right ventricular cardiomyopathy Mus musculus mmu05412",0.144552041430675,0.311000284950191,0.0851793600446299
|
| 345 |
+
"Dilated cardiomyopathy Mus musculus mmu05414",0.00131421890755068,0.0103025015642693,0.00285002066115343
|
| 346 |
+
"Diabetic cardiomyopathy Mus musculus mmu05415",2.03241237889416e-08,0.239621576699231,0.00152320077995881
|
| 347 |
+
"Viral myocarditis Mus musculus mmu05416",3.12454954518457e-20,0.328683440209422,0.0954703335679758
|
| 348 |
+
"Type II diabetes mellitus Mus musculus mmu04930",3.65115193842386e-05,0.187695284442053,1
|
| 349 |
+
"Type I diabetes mellitus Mus musculus mmu04940",2.95609384368751e-18,0.032398480049453,0.0523069824664406
|
| 350 |
+
"Maturity onset diabetes of the young Mus musculus mmu04950",0.190083747808751,0.11034487561601,1
|
| 351 |
+
"Alcoholic liver disease Mus musculus mmu04936",7.7700501442954e-12,0.00340780348519291,0.0086070583454657
|
| 352 |
+
"Non-alcoholic fatty liver disease Mus musculus mmu04932",0.000302134222922943,0.155477403411605,0.0137615868731135
|
| 353 |
+
"Insulin resistance Mus musculus mmu04931",2.6416902701107e-06,0.0823832704917093,0.0036084634732197
|
| 354 |
+
"AGE-RAGE signaling pathway in diabetic complications Mus musculus mmu04933",7.34083809331016e-14,1,0.019783574893119
|
| 355 |
+
"Cushing syndrome Mus musculus mmu04934",4.46906708943513e-05,0.000738850610984965,0.00237239082116221
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/run_metadata.json
ADDED
|
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+
{
|
| 2 |
+
"task_id": "alzheimer-mouse",
|
| 3 |
+
"task_name": "Alzheimer Mouse Models: Comparative Pathway Analysis",
|
| 4 |
+
"run_dir": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905",
|
| 5 |
+
"dataset_dir": "/225040511/project/bioagent-bench/dataset/alzheimer-mouse",
|
| 6 |
+
"data_dir": "/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data",
|
| 7 |
+
"reference_dir": "/225040511/project/bioagent-bench/dataset/alzheimer-mouse/reference",
|
| 8 |
+
"agent_runtime_dir": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/agent_runtime",
|
| 9 |
+
"output_paths": [
|
| 10 |
+
"/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv"
|
| 11 |
+
],
|
| 12 |
+
"mcp_config": "/225040511/project/Biomni/experiments/bioagent_bench/configs/mcp_scale_1000.yaml",
|
| 13 |
+
"agent_kwargs": {
|
| 14 |
+
"path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/agent_runtime",
|
| 15 |
+
"expected_data_lake_files": [],
|
| 16 |
+
"use_tool_retriever": true,
|
| 17 |
+
"timeout_seconds": 1200,
|
| 18 |
+
"llm": "deepseek-v4-flash",
|
| 19 |
+
"source": "Custom",
|
| 20 |
+
"base_url": "https://api.deepseek.com/v1",
|
| 21 |
+
"api_key": "sk-06e6154722b84e89b081b1c9571838ef"
|
| 22 |
+
},
|
| 23 |
+
"query": "You are running a bioagent-bench task with local files already prepared.\n\nTask ID: alzheimer-mouse\nTask name: Alzheimer Mouse Models: Comparative Pathway Analysis\nBenchmark prompt:\nPerform a comparative differential expression analysis of three different Alzheimer's Disease mouse models (5xFAD, 3xTG-AD, and PS3O1S) to identify shared molecular KEGG pathways. The output should be a CSV file with the following columns: 'pathway','5xFAD_pvalue','3xTG_AD_pvalue','PS3O1S_pvalue'. Example csv <example>Pathway,5xFAD_pvalue,3xTG_AD_pvalue,PS3O1S_pvalue\nPhagosome Homo sapiens hsa04145,1.5045916403148935e-09,0.3102788532065793,0.4443015705596512\n</example> \nData background:\nAnalyze 5xFAD, 3xTG-AD, and PS301S mouse models: normalize counts, perform differential expression, run KEGG pathway enrichment, and compare shared pathways across models.\n\nConstraints:\n1. Use only the benchmark inputs and references explicitly listed below.\n2. Save the required final deliverables exactly to the paths listed below.\n3. Save all intermediate scripts, logs, and scratch outputs inside this run directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905\n4. Keep final deliverables in the same schema/format requested by the benchmark prompt.\n5. Return a concise final summary after writing the required files.\n\nTask-specific instruction:\nUse the provided mouse count and DEA files as inputs. Report the shared/comparative KEGG pathway set supported by the three model analyses, with the requested pathway and p-value columns.\n\nBenchmark data policy:\n- Allowed input data directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data\n- Allowed reference directory: <none>\n- Allowed scratch/output directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905\n- Forbidden truth/results directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/results\n- Forbidden sibling benchmark task directories: /225040511/project/bioagent-bench/dataset/<any task other than alzheimer-mouse>\n- Do not inspect previous bioagent-bench-runs or sibling task outputs as data sources.\n- Do not download external databases or install new packages during the benchmark run.\n\nInput data directory:\n/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data\nVisible input files:\n- DEA_PS3O1S.csv\n- GSE161904_Raw_gene_counts_cortex.txt\n- GSE168137_countList.txt\n\nReference data directory:\n<none>\nVisible reference files:\n- <none>\n\nRequired final output paths:\n- pathway_comparison.csv: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv",
|
| 24 |
+
"timestamp_utc": "20260515_134905",
|
| 25 |
+
"runtime_environment": {
|
| 26 |
+
"execution_env_prefix": "/225040511/miniconda3/envs/biomni_e1",
|
| 27 |
+
"execution_python": "/225040511/miniconda3/envs/biomni_e1/bin/python",
|
| 28 |
+
"conda_default_env": "biomni_e1",
|
| 29 |
+
"conda_prefix": "/225040511/miniconda3/envs/biomni_e1"
|
| 30 |
+
},
|
| 31 |
+
"biomni_root": "/225040511/project/Biomni"
|
| 32 |
+
}
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/run_summary.json
ADDED
|
@@ -0,0 +1,17 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"task_id": "alzheimer-mouse",
|
| 3 |
+
"run_dir": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905",
|
| 4 |
+
"outputs": [
|
| 5 |
+
{
|
| 6 |
+
"path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv",
|
| 7 |
+
"exists": true,
|
| 8 |
+
"size_bytes": 35447
|
| 9 |
+
}
|
| 10 |
+
],
|
| 11 |
+
"planning_latency_seconds": 29.027789920568466,
|
| 12 |
+
"total_runtime_seconds": 534.293803807348,
|
| 13 |
+
"final_answer_path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/final_answer.txt",
|
| 14 |
+
"metadata_path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/run_metadata.json",
|
| 15 |
+
"retrieval_plan_path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/retrieval_plan.json",
|
| 16 |
+
"output_validation_path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/output_validation.json"
|
| 17 |
+
}
|
experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/task_query.txt
ADDED
|
@@ -0,0 +1,44 @@
|
|
|
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|
|
|
|
|
|
|
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|
|
|
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|
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|
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|
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|
|
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|
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|
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|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
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|
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|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
| 1 |
+
You are running a bioagent-bench task with local files already prepared.
|
| 2 |
+
|
| 3 |
+
Task ID: alzheimer-mouse
|
| 4 |
+
Task name: Alzheimer Mouse Models: Comparative Pathway Analysis
|
| 5 |
+
Benchmark prompt:
|
| 6 |
+
Perform a comparative differential expression analysis of three different Alzheimer's Disease mouse models (5xFAD, 3xTG-AD, and PS3O1S) to identify shared molecular KEGG pathways. The output should be a CSV file with the following columns: 'pathway','5xFAD_pvalue','3xTG_AD_pvalue','PS3O1S_pvalue'. Example csv <example>Pathway,5xFAD_pvalue,3xTG_AD_pvalue,PS3O1S_pvalue
|
| 7 |
+
Phagosome Homo sapiens hsa04145,1.5045916403148935e-09,0.3102788532065793,0.4443015705596512
|
| 8 |
+
</example>
|
| 9 |
+
Data background:
|
| 10 |
+
Analyze 5xFAD, 3xTG-AD, and PS301S mouse models: normalize counts, perform differential expression, run KEGG pathway enrichment, and compare shared pathways across models.
|
| 11 |
+
|
| 12 |
+
Constraints:
|
| 13 |
+
1. Use only the benchmark inputs and references explicitly listed below.
|
| 14 |
+
2. Save the required final deliverables exactly to the paths listed below.
|
| 15 |
+
3. Save all intermediate scripts, logs, and scratch outputs inside this run directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905
|
| 16 |
+
4. Keep final deliverables in the same schema/format requested by the benchmark prompt.
|
| 17 |
+
5. Return a concise final summary after writing the required files.
|
| 18 |
+
|
| 19 |
+
Task-specific instruction:
|
| 20 |
+
Use the provided mouse count and DEA files as inputs. Report the shared/comparative KEGG pathway set supported by the three model analyses, with the requested pathway and p-value columns.
|
| 21 |
+
|
| 22 |
+
Benchmark data policy:
|
| 23 |
+
- Allowed input data directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/data
|
| 24 |
+
- Allowed reference directory: <none>
|
| 25 |
+
- Allowed scratch/output directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905
|
| 26 |
+
- Forbidden truth/results directory: /225040511/project/bioagent-bench/dataset/alzheimer-mouse/results
|
| 27 |
+
- Forbidden sibling benchmark task directories: /225040511/project/bioagent-bench/dataset/<any task other than alzheimer-mouse>
|
| 28 |
+
- Do not inspect previous bioagent-bench-runs or sibling task outputs as data sources.
|
| 29 |
+
- Do not download external databases or install new packages during the benchmark run.
|
| 30 |
+
|
| 31 |
+
Input data directory:
|
| 32 |
+
/225040511/project/bioagent-bench/dataset/alzheimer-mouse/data
|
| 33 |
+
Visible input files:
|
| 34 |
+
- DEA_PS3O1S.csv
|
| 35 |
+
- GSE161904_Raw_gene_counts_cortex.txt
|
| 36 |
+
- GSE168137_countList.txt
|
| 37 |
+
|
| 38 |
+
Reference data directory:
|
| 39 |
+
<none>
|
| 40 |
+
Visible reference files:
|
| 41 |
+
- <none>
|
| 42 |
+
|
| 43 |
+
Required final output paths:
|
| 44 |
+
- pathway_comparison.csv: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/alzheimer-mouse_20260515_134905/pathway_comparison.csv
|
experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135339/decode_alphabet.R
ADDED
|
@@ -0,0 +1,39 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
|
| 2 |
+
load("/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135339/Actinobacteria_decompressed.RData")
|
| 3 |
+
|
| 4 |
+
# The reduced alphabet encoding (KEGG standard for KofamKOALA)
|
| 5 |
+
# alphabet has length 20, values 0-5 mapping to groups
|
| 6 |
+
# Standard KEGG reduced alphabet:
|
| 7 |
+
# 0 = A,G,V,I,L (aliphatic)
|
| 8 |
+
# 1 = F,Y,W (aromatic)
|
| 9 |
+
# 2 = K,R,H (basic)
|
| 10 |
+
# 3 = D,E (acidic)
|
| 11 |
+
# 4 = Q,N,S,T (polar uncharged)
|
| 12 |
+
# 5 = P,C,M (special)
|
| 13 |
+
# But we need to check the actual mapping
|
| 14 |
+
|
| 15 |
+
alph <- trainingSet$alphabet
|
| 16 |
+
cat("alphabet (length 20, for 20 standard amino acids):\n")
|
| 17 |
+
cat("Index: ", 1:20, "\n")
|
| 18 |
+
cat("Value: ", alph, "\n")
|
| 19 |
+
|
| 20 |
+
# Standard amino acid order: A C D E F G H I K L M N P Q R S T V W Y
|
| 21 |
+
# This is the default order in bioinformatics
|
| 22 |
+
aa_order <- c("A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y")
|
| 23 |
+
for(i in 1:20) {
|
| 24 |
+
cat(aa_order[i], "->", alph[i], "\n")
|
| 25 |
+
}
|
| 26 |
+
|
| 27 |
+
# So the groups are:
|
| 28 |
+
# Group 0: A, C, D, E, G (index 1-5,7)
|
| 29 |
+
# Group 1: F, H (index 6,8)
|
| 30 |
+
# Group 2: K (index 10)
|
| 31 |
+
# Group 3: R (index 15)
|
| 32 |
+
# Group 4: L, N, P, Q, S (index 11,13,14,16)
|
| 33 |
+
# Wait, let me re-check...
|
| 34 |
+
cat("\nUnique groups:", unique(alph), "\n")
|
| 35 |
+
cat("Group assignment:\n")
|
| 36 |
+
for(g in sort(unique(alph))) {
|
| 37 |
+
aas <- aa_order[alph == g]
|
| 38 |
+
cat(" Group", g, ":", paste(aas, collapse=","), "\n")
|
| 39 |
+
}
|
experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135339/extract_model2.R
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
|
| 2 |
+
library(base)
|
| 3 |
+
|
| 4 |
+
load("/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135339/Actinobacteria_decompressed.RData")
|
| 5 |
+
|
| 6 |
+
cat("Object trainingSet exists:", exists("trainingSet"), "\n")
|
| 7 |
+
cat("Class:", class(trainingSet)[1], "\n")
|
| 8 |
+
cat("names:", paste(names(trainingSet), collapse=", "), "\n")
|
| 9 |
+
|
| 10 |
+
# Save IDF weights
|
| 11 |
+
saveRDS(trainingSet$IDFweights, file="/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135339/idf_weights.rds")
|
| 12 |
+
cat("IDFweights saved, length:", length(trainingSet$IDFweights), "\n")
|
| 13 |
+
|
| 14 |
+
# Save taxonomy info
|
| 15 |
+
saveRDS(list(
|
| 16 |
+
taxonomy = trainingSet$taxonomy,
|
| 17 |
+
taxa = trainingSet$taxa,
|
| 18 |
+
K = trainingSet$K,
|
| 19 |
+
alphabet = trainingSet$alphabet
|
| 20 |
+
), file="/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135339/model_meta.rds")
|
| 21 |
+
cat("Model metadata saved\n")
|
experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135339/inspect_rdata.R
ADDED
|
@@ -0,0 +1,34 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
|
| 2 |
+
library(stringr)
|
| 3 |
+
|
| 4 |
+
# Load the RData
|
| 5 |
+
load("/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/comparative-genomics_20260515_135339/Actinobacteria_decompressed.RData")
|
| 6 |
+
print(ls())
|
| 7 |
+
print("---")
|
| 8 |
+
for(obj_name in ls()) {
|
| 9 |
+
obj <- get(obj_name)
|
| 10 |
+
cat("Object:", obj_name, "- class:", class(obj), "
|
| 11 |
+
")
|
| 12 |
+
if(is.data.frame(obj)) {
|
| 13 |
+
cat(" Dimensions:", nrow(obj), "x", ncol(obj), "
|
| 14 |
+
")
|
| 15 |
+
cat(" Column names:", paste(head(colnames(obj)), collapse=", "), "
|
| 16 |
+
")
|
| 17 |
+
cat(" First few rows:
|
| 18 |
+
")
|
| 19 |
+
print(head(obj, 3))
|
| 20 |
+
} else if(is.list(obj) && !is.data.frame(obj)) {
|
| 21 |
+
cat(" Length:", length(obj), "
|
| 22 |
+
")
|
| 23 |
+
cat(" Names:", paste(head(names(obj)), collapse=", "), "
|
| 24 |
+
")
|
| 25 |
+
} else if(is.matrix(obj)) {
|
| 26 |
+
cat(" Dimensions:", nrow(obj), "x", ncol(obj), "
|
| 27 |
+
")
|
| 28 |
+
cat(" First few rows:
|
| 29 |
+
")
|
| 30 |
+
print(head(obj, 3))
|
| 31 |
+
}
|
| 32 |
+
cat("---
|
| 33 |
+
")
|
| 34 |
+
}
|
experiments/bioagent_bench/runs/scale_1000/cystic-fibrosis_20260515_141940/retrieval_plan.json
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
experiments/bioagent_bench/runs/scale_1000/cystic-fibrosis_20260515_141940/run_metadata.json
ADDED
|
@@ -0,0 +1,32 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"task_id": "cystic-fibrosis",
|
| 3 |
+
"task_name": "Cystic Fibrosis Mendelian Variant Identification",
|
| 4 |
+
"run_dir": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/cystic-fibrosis_20260515_141940",
|
| 5 |
+
"dataset_dir": "/225040511/project/bioagent-bench/dataset/cystic-fibrosis",
|
| 6 |
+
"data_dir": "/225040511/project/bioagent-bench/dataset/cystic-fibrosis/data",
|
| 7 |
+
"reference_dir": "/225040511/project/bioagent-bench/dataset/cystic-fibrosis/reference",
|
| 8 |
+
"agent_runtime_dir": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/cystic-fibrosis_20260515_141940/agent_runtime",
|
| 9 |
+
"output_paths": [
|
| 10 |
+
"/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/cystic-fibrosis_20260515_141940/cf_variants.csv"
|
| 11 |
+
],
|
| 12 |
+
"mcp_config": "/225040511/project/Biomni/experiments/bioagent_bench/configs/mcp_scale_1000.yaml",
|
| 13 |
+
"agent_kwargs": {
|
| 14 |
+
"path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/cystic-fibrosis_20260515_141940/agent_runtime",
|
| 15 |
+
"expected_data_lake_files": [],
|
| 16 |
+
"use_tool_retriever": true,
|
| 17 |
+
"timeout_seconds": 1200,
|
| 18 |
+
"llm": "deepseek-v4-flash",
|
| 19 |
+
"source": "Custom",
|
| 20 |
+
"base_url": "https://api.deepseek.com/v1",
|
| 21 |
+
"api_key": "sk-06e6154722b84e89b081b1c9571838ef"
|
| 22 |
+
},
|
| 23 |
+
"query": "You are running a bioagent-bench task with local files already prepared.\n\nTask ID: cystic-fibrosis\nTask name: Cystic Fibrosis Mendelian Variant Identification\nBenchmark prompt:\nFind the genetic cause of Cystic fibrosis; identify the causal recessive variant consistent with affected siblings NA12885, NA12886, and NA12879. The output should be a CSV file with the following columns: chromosome,position,variant_id,reference,alternate,gene_name,gene_id,annotation,impact,transcript_id,hgvs_c,hgvs_p,clinical_significance,diseases,review_status,rs_id. <example>chromosome,position,variant_id,reference,alternate,gene_name,gene_id,annotation,impact,transcript_id,hgvs_c,hgvs_p,clinical_significance,diseases,review_status,rs_id\nX,123456789,VAR123,A,G,GENE1,ENSG00000000001,missense_variant,MODERATE,ENST00000000001,c.123A>G,p.Lys41Arg,Likely_pathogenic,Disease_A; Disease_B; not_provided,reviewed_by_expert_panel,rs0000001</example>\nData background:\nThe sample dataset is a simulated dataset for finding the genetic cause of Cystic fibrosis. The dataset is real sequencing data from CEPH_1463 dataset provided by the Complete Genomics Diversity Panel. It consists of sequencing of a family: 4 grandparents, 2 parents and 11 siblings. A known Mandelian disease mutation has been added on three siblings, taking care to be consistent with the underlying heplotype structure. The goal is to find the mutation causing the mendalian recessive trait - Cystic Fibrosis.\n\nConstraints:\n1. Use only the benchmark inputs and references explicitly listed below.\n2. Save the required final deliverables exactly to the paths listed below.\n3. Save all intermediate scripts, logs, and scratch outputs inside this run directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/cystic-fibrosis_20260515_141940\n4. Keep final deliverables in the same schema/format requested by the benchmark prompt.\n5. Return a concise final summary after writing the required files.\n\nTask-specific instruction:\nUse only the provided family variant data and ClinVar VCF. The final row should identify the causal CFTR recessive variant consistent with affected siblings.\n\nBenchmark data policy:\n- Allowed input data directory: /225040511/project/bioagent-bench/dataset/cystic-fibrosis/data\n- Allowed reference directory: /225040511/project/bioagent-bench/dataset/cystic-fibrosis/reference\n- Allowed scratch/output directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/cystic-fibrosis_20260515_141940\n- Forbidden truth/results directory: /225040511/project/bioagent-bench/dataset/cystic-fibrosis/results\n- Forbidden sibling benchmark task directories: /225040511/project/bioagent-bench/dataset/<any task other than cystic-fibrosis>\n- Do not inspect previous bioagent-bench-runs or sibling task outputs as data sources.\n- Do not download external databases or install new packages during the benchmark run.\n\nInput data directory:\n/225040511/project/bioagent-bench/dataset/cystic-fibrosis/data\nVisible input files:\n- ex1.eff.vcf.gz\n- ex1.eff.vcf.gz.tbi\n- family_description.txt\n\nReference data directory:\n/225040511/project/bioagent-bench/dataset/cystic-fibrosis/reference\nVisible reference files:\n- clinvar_20250521.vcf.gz\n- clinvar_20250521.vcf.gz.tbi\n\nRequired final output paths:\n- cf_variants.csv: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/cystic-fibrosis_20260515_141940/cf_variants.csv",
|
| 24 |
+
"timestamp_utc": "20260515_141940",
|
| 25 |
+
"runtime_environment": {
|
| 26 |
+
"execution_env_prefix": "/225040511/miniconda3/envs/biomni_e1",
|
| 27 |
+
"execution_python": "/225040511/miniconda3/envs/biomni_e1/bin/python",
|
| 28 |
+
"conda_default_env": "biomni_e1",
|
| 29 |
+
"conda_prefix": "/225040511/miniconda3/envs/biomni_e1"
|
| 30 |
+
},
|
| 31 |
+
"biomni_root": "/225040511/project/Biomni"
|
| 32 |
+
}
|
experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/anc_reference.amb
ADDED
|
@@ -0,0 +1,11 @@
|
|
|
|
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|
|
|
|
|
|
|
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|
|
| 1 |
+
4553797 304 10
|
| 2 |
+
205933 10 N
|
| 3 |
+
725746 10 N
|
| 4 |
+
735427 10 N
|
| 5 |
+
1249452 100 N
|
| 6 |
+
1345489 100 N
|
| 7 |
+
1449271 100 N
|
| 8 |
+
1609219 100 N
|
| 9 |
+
1786047 100 N
|
| 10 |
+
3224701 100 N
|
| 11 |
+
3578146 100 N
|
experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/anc_reference.ann
ADDED
|
@@ -0,0 +1,609 @@
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|
|
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|
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|
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|
|
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|
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|
|
|
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|
|
|
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|
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|
|
|
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|
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|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
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|
|
|
|
|
| 1 |
+
4553797 304 11
|
| 2 |
+
0 NODE_1_length_157883_cov_5.792245 (null)
|
| 3 |
+
0 157883 0
|
| 4 |
+
0 NODE_2_length_136556_cov_6.058610 (null)
|
| 5 |
+
157883 136556 1
|
| 6 |
+
0 NODE_3_length_120662_cov_5.793225 (null)
|
| 7 |
+
294439 120662 0
|
| 8 |
+
0 NODE_4_length_115200_cov_5.646674 (null)
|
| 9 |
+
415101 115200 0
|
| 10 |
+
0 NODE_5_length_100986_cov_5.887790 (null)
|
| 11 |
+
530301 100986 0
|
| 12 |
+
0 NODE_6_length_99436_cov_6.313812 (null)
|
| 13 |
+
631287 99436 1
|
| 14 |
+
0 NODE_7_length_98767_cov_6.178630 (null)
|
| 15 |
+
730723 98767 1
|
| 16 |
+
0 NODE_8_length_94611_cov_6.250206 (null)
|
| 17 |
+
829490 94611 0
|
| 18 |
+
0 NODE_9_length_94175_cov_5.661884 (null)
|
| 19 |
+
924101 94175 0
|
| 20 |
+
0 NODE_10_length_90906_cov_5.832487 (null)
|
| 21 |
+
1018276 90906 0
|
| 22 |
+
0 NODE_11_length_88167_cov_5.630299 (null)
|
| 23 |
+
1109182 88167 0
|
| 24 |
+
0 NODE_12_length_87061_cov_5.654327 (null)
|
| 25 |
+
1197349 87061 1
|
| 26 |
+
0 NODE_13_length_82774_cov_5.647823 (null)
|
| 27 |
+
1284410 82774 1
|
| 28 |
+
0 NODE_14_length_82265_cov_6.047038 (null)
|
| 29 |
+
1367184 82265 1
|
| 30 |
+
0 NODE_15_length_73417_cov_5.715858 (null)
|
| 31 |
+
1449449 73417 0
|
| 32 |
+
0 NODE_16_length_73230_cov_5.791164 (null)
|
| 33 |
+
1522866 73230 0
|
| 34 |
+
0 NODE_17_length_72820_cov_5.747880 (null)
|
| 35 |
+
1596096 72820 1
|
| 36 |
+
0 NODE_18_length_72278_cov_5.854614 (null)
|
| 37 |
+
1668916 72278 0
|
| 38 |
+
0 NODE_19_length_68730_cov_5.620614 (null)
|
| 39 |
+
1741194 68730 1
|
| 40 |
+
0 NODE_20_length_68650_cov_6.114827 (null)
|
| 41 |
+
1809924 68650 0
|
| 42 |
+
0 NODE_21_length_67561_cov_5.758076 (null)
|
| 43 |
+
1878574 67561 0
|
| 44 |
+
0 NODE_22_length_66904_cov_6.051566 (null)
|
| 45 |
+
1946135 66904 0
|
| 46 |
+
0 NODE_23_length_66480_cov_5.901495 (null)
|
| 47 |
+
2013039 66480 0
|
| 48 |
+
0 NODE_24_length_64464_cov_5.667511 (null)
|
| 49 |
+
2079519 64464 0
|
| 50 |
+
0 NODE_25_length_61996_cov_6.408033 (null)
|
| 51 |
+
2143983 61996 0
|
| 52 |
+
0 NODE_26_length_60681_cov_5.742228 (null)
|
| 53 |
+
2205979 60681 0
|
| 54 |
+
0 NODE_27_length_60506_cov_5.955468 (null)
|
| 55 |
+
2266660 60506 0
|
| 56 |
+
0 NODE_28_length_57404_cov_5.750449 (null)
|
| 57 |
+
2327166 57404 0
|
| 58 |
+
0 NODE_29_length_51960_cov_5.819980 (null)
|
| 59 |
+
2384570 51960 0
|
| 60 |
+
0 NODE_30_length_50016_cov_5.992411 (null)
|
| 61 |
+
2436530 50016 0
|
| 62 |
+
0 NODE_31_length_47605_cov_5.967303 (null)
|
| 63 |
+
2486546 47605 0
|
| 64 |
+
0 NODE_32_length_46513_cov_5.649108 (null)
|
| 65 |
+
2534151 46513 0
|
| 66 |
+
0 NODE_33_length_45630_cov_6.165565 (null)
|
| 67 |
+
2580664 45630 0
|
| 68 |
+
0 NODE_34_length_44235_cov_6.126885 (null)
|
| 69 |
+
2626294 44235 0
|
| 70 |
+
0 NODE_35_length_44031_cov_5.889703 (null)
|
| 71 |
+
2670529 44031 0
|
| 72 |
+
0 NODE_36_length_40559_cov_6.072650 (null)
|
| 73 |
+
2714560 40559 0
|
| 74 |
+
0 NODE_37_length_38821_cov_6.129388 (null)
|
| 75 |
+
2755119 38821 0
|
| 76 |
+
0 NODE_38_length_38644_cov_5.892006 (null)
|
| 77 |
+
2793940 38644 0
|
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experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/anc_reference.fasta.fai
ADDED
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@@ -0,0 +1,304 @@
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experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/ancestor.raw.vcf
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/ancestor.sorted.bam.bai
ADDED
|
Binary file (32.9 kB). View file
|
|
|
experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/annotate_variants.py
ADDED
|
@@ -0,0 +1,244 @@
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|
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|
|
|
|
|
|
|
|
|
| 1 |
+
|
| 2 |
+
import os, sys
|
| 3 |
+
from Bio import SeqIO
|
| 4 |
+
from Bio.Seq import Seq
|
| 5 |
+
import csv
|
| 6 |
+
|
| 7 |
+
run_dir = "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912"
|
| 8 |
+
ref_fasta = os.path.join(run_dir, "anc_reference.fasta")
|
| 9 |
+
gff_path = os.path.join(run_dir, "prokka_annotation", "ecoli_ref.gff")
|
| 10 |
+
|
| 11 |
+
# Load reference genome
|
| 12 |
+
ref_seqs = {}
|
| 13 |
+
for record in SeqIO.parse(ref_fasta, "fasta"):
|
| 14 |
+
ref_seqs[record.id] = str(record.seq)
|
| 15 |
+
|
| 16 |
+
# Load CDS features from GFF
|
| 17 |
+
cds_features = []
|
| 18 |
+
with open(gff_path) as f:
|
| 19 |
+
for line in f:
|
| 20 |
+
if line.startswith('#'):
|
| 21 |
+
continue
|
| 22 |
+
parts = line.strip().split('\t')
|
| 23 |
+
if len(parts) >= 9:
|
| 24 |
+
chrom = parts[0]
|
| 25 |
+
feat_type = parts[2]
|
| 26 |
+
start = int(parts[3])
|
| 27 |
+
end = int(parts[4])
|
| 28 |
+
strand = parts[6]
|
| 29 |
+
attrs = parts[8]
|
| 30 |
+
|
| 31 |
+
attr_dict = {}
|
| 32 |
+
for attr in attrs.split(';'):
|
| 33 |
+
if '=' in attr:
|
| 34 |
+
k, v = attr.split('=', 1)
|
| 35 |
+
attr_dict[k] = v
|
| 36 |
+
|
| 37 |
+
if feat_type == 'CDS':
|
| 38 |
+
gene_name = attr_dict.get('gene', '')
|
| 39 |
+
locus_tag = attr_dict.get('locus_tag', '')
|
| 40 |
+
cds_features.append({
|
| 41 |
+
'chrom': chrom, 'start': start, 'end': end,
|
| 42 |
+
'strand': strand, 'gene': gene_name,
|
| 43 |
+
'locus_tag': locus_tag
|
| 44 |
+
})
|
| 45 |
+
|
| 46 |
+
print(f"Loaded {len(cds_features)} CDS features")
|
| 47 |
+
print(f"Loaded {len(ref_seqs)} reference sequences")
|
| 48 |
+
|
| 49 |
+
def find_overlapping_gene(chrom, pos, cds_list):
|
| 50 |
+
"""Find if a position overlaps with any CDS feature"""
|
| 51 |
+
overlapping = []
|
| 52 |
+
for cds in cds_list:
|
| 53 |
+
if cds['chrom'] == chrom and cds['start'] <= pos <= cds['end']:
|
| 54 |
+
overlapping.append(cds)
|
| 55 |
+
return overlapping
|
| 56 |
+
|
| 57 |
+
def determine_variant_effect(chrom, pos, ref, alt, ref_seqs, cds_list):
|
| 58 |
+
"""Determine the effect of a variant"""
|
| 59 |
+
genes_hit = find_overlapping_gene(chrom, pos, cds_list)
|
| 60 |
+
|
| 61 |
+
if not genes_hit:
|
| 62 |
+
# Check if close to a gene (upstream/downstream - within 500bp)
|
| 63 |
+
nearby = [cds for cds in cds_list
|
| 64 |
+
if cds['chrom'] == chrom and
|
| 65 |
+
abs(cds['start'] - pos) <= 500 and cds['start'] > pos]
|
| 66 |
+
nearby2 = [cds for cds in cds_list
|
| 67 |
+
if cds['chrom'] == chrom and
|
| 68 |
+
abs(pos - cds['end']) <= 500 and cds['end'] < pos]
|
| 69 |
+
if nearby or nearby2:
|
| 70 |
+
all_near = nearby + nearby2
|
| 71 |
+
all_genes = [n['gene'] for n in all_near if n['gene']]
|
| 72 |
+
return ('MODIFIER', 'upstream_gene_variant', all_genes[0] if all_genes else 'unknown')
|
| 73 |
+
return ('MODIFIER', 'intergenic_region', '')
|
| 74 |
+
|
| 75 |
+
# Found in a CDS
|
| 76 |
+
cds = genes_hit[0]
|
| 77 |
+
gene = cds['gene'] if cds['gene'] else cds['locus_tag']
|
| 78 |
+
strand = cds['strand']
|
| 79 |
+
|
| 80 |
+
# Simple SNP
|
| 81 |
+
if len(ref) == 1 and len(alt) == 1:
|
| 82 |
+
try:
|
| 83 |
+
chrom_seq = ref_seqs.get(chrom, '')
|
| 84 |
+
if chrom_seq:
|
| 85 |
+
# Get the CDS sequence
|
| 86 |
+
if strand == '+':
|
| 87 |
+
cds_seq = chrom_seq[cds['start']-1:cds['end']]
|
| 88 |
+
else:
|
| 89 |
+
cds_seq = str(Seq(chrom_seq[cds['start']-1:cds['end']]).reverse_complement())
|
| 90 |
+
|
| 91 |
+
# Position within CDS (0-indexed)
|
| 92 |
+
if strand == '+':
|
| 93 |
+
rel_pos = pos - cds['start']
|
| 94 |
+
else:
|
| 95 |
+
rel_pos = cds['end'] - pos
|
| 96 |
+
|
| 97 |
+
codon_start = (rel_pos // 3) * 3
|
| 98 |
+
|
| 99 |
+
if codon_start + 3 <= len(cds_seq):
|
| 100 |
+
original_codon = cds_seq[codon_start:codon_start+3]
|
| 101 |
+
base_in_codon = rel_pos % 3
|
| 102 |
+
|
| 103 |
+
# Get alt base in CDS orientation
|
| 104 |
+
if strand == '+':
|
| 105 |
+
alt_base = alt
|
| 106 |
+
else:
|
| 107 |
+
alt_base = str(Seq(alt).reverse_complement())
|
| 108 |
+
|
| 109 |
+
new_codon = list(original_codon)
|
| 110 |
+
if base_in_codon < len(new_codon):
|
| 111 |
+
new_codon[base_in_codon] = alt_base
|
| 112 |
+
new_codon_str = ''.join(new_codon)
|
| 113 |
+
|
| 114 |
+
orig_aa = str(Seq(original_codon).translate(table='Bacterial'))
|
| 115 |
+
new_aa = str(Seq(new_codon_str).translate(table='Bacterial'))
|
| 116 |
+
|
| 117 |
+
if orig_aa == new_aa:
|
| 118 |
+
return ('LOW', 'synonymous_variant', gene)
|
| 119 |
+
elif new_aa == '*':
|
| 120 |
+
return ('HIGH', 'stop_gained', gene)
|
| 121 |
+
elif orig_aa == '*':
|
| 122 |
+
return ('HIGH', 'stop_lost', gene)
|
| 123 |
+
else:
|
| 124 |
+
return ('MODERATE', 'missense_variant', gene)
|
| 125 |
+
else:
|
| 126 |
+
# Near CDS boundary
|
| 127 |
+
return ('LOW', 'coding_sequence_variant', gene)
|
| 128 |
+
except Exception as e:
|
| 129 |
+
pass
|
| 130 |
+
|
| 131 |
+
return ('MODERATE', 'missense_variant', gene)
|
| 132 |
+
|
| 133 |
+
elif len(ref) > 1 or len(alt) > 1:
|
| 134 |
+
# Indel
|
| 135 |
+
if len(ref) > len(alt):
|
| 136 |
+
diff = len(ref) - len(alt)
|
| 137 |
+
if diff % 3 == 0:
|
| 138 |
+
return ('MODERATE', 'inframe_deletion', gene)
|
| 139 |
+
else:
|
| 140 |
+
return ('HIGH', 'frameshift_variant', gene)
|
| 141 |
+
elif len(alt) > len(ref):
|
| 142 |
+
diff = len(alt) - len(ref)
|
| 143 |
+
if diff % 3 == 0:
|
| 144 |
+
return ('MODERATE', 'inframe_insertion', gene)
|
| 145 |
+
else:
|
| 146 |
+
return ('HIGH', 'frameshift_variant', gene)
|
| 147 |
+
else:
|
| 148 |
+
return ('MODERATE', 'missense_variant', gene)
|
| 149 |
+
|
| 150 |
+
return ('MODIFIER', 'coding_sequence_variant', gene)
|
| 151 |
+
|
| 152 |
+
# Parse VCFs
|
| 153 |
+
def parse_vcf(vcf_path):
|
| 154 |
+
variants = set()
|
| 155 |
+
with open(vcf_path) as f:
|
| 156 |
+
for line in f:
|
| 157 |
+
if line.startswith('#'):
|
| 158 |
+
continue
|
| 159 |
+
parts = line.strip().split('\t')
|
| 160 |
+
if len(parts) < 5:
|
| 161 |
+
continue
|
| 162 |
+
chrom = parts[0]
|
| 163 |
+
pos = int(parts[1])
|
| 164 |
+
ref = parts[3]
|
| 165 |
+
alt = parts[4]
|
| 166 |
+
for a in alt.split(','):
|
| 167 |
+
variants.add((chrom, pos, ref, a))
|
| 168 |
+
return variants
|
| 169 |
+
|
| 170 |
+
anc_variants = parse_vcf(os.path.join(run_dir, "ancestor.raw.vcf"))
|
| 171 |
+
evol1_variants = parse_vcf(os.path.join(run_dir, "evol1.raw.vcf"))
|
| 172 |
+
evol2_variants = parse_vcf(os.path.join(run_dir, "evol2.raw.vcf"))
|
| 173 |
+
|
| 174 |
+
print(f"Ancestor: {len(anc_variants)} variants")
|
| 175 |
+
print(f"Evol1: {len(evol1_variants)} variants")
|
| 176 |
+
print(f"Evol2: {len(evol2_variants)} variants")
|
| 177 |
+
|
| 178 |
+
# Find shared + new
|
| 179 |
+
shared = evol1_variants & evol2_variants
|
| 180 |
+
new_variants = shared - anc_variants
|
| 181 |
+
|
| 182 |
+
print(f"Shared by both evolved: {len(shared)}")
|
| 183 |
+
print(f"New (not in ancestor): {len(new_variants)}")
|
| 184 |
+
|
| 185 |
+
# Annotate each variant
|
| 186 |
+
results = []
|
| 187 |
+
gene_annotations = []
|
| 188 |
+
for chrom, pos, ref, alt in sorted(new_variants):
|
| 189 |
+
impact, effect, gene = determine_variant_effect(chrom, pos, ref, alt, ref_seqs, cds_features)
|
| 190 |
+
|
| 191 |
+
results.append({
|
| 192 |
+
'chrom': chrom,
|
| 193 |
+
'pos': str(pos),
|
| 194 |
+
'ref': ref,
|
| 195 |
+
'alt': alt,
|
| 196 |
+
'gene': gene,
|
| 197 |
+
'impact': impact,
|
| 198 |
+
'effect': effect,
|
| 199 |
+
'status': 'shared'
|
| 200 |
+
})
|
| 201 |
+
|
| 202 |
+
if gene:
|
| 203 |
+
gene_annotations.append({
|
| 204 |
+
'chrom': chrom,
|
| 205 |
+
'pos': pos,
|
| 206 |
+
'ref': ref,
|
| 207 |
+
'alt': alt,
|
| 208 |
+
'gene': gene,
|
| 209 |
+
'impact': impact,
|
| 210 |
+
'effect': effect
|
| 211 |
+
})
|
| 212 |
+
|
| 213 |
+
# Filter for moderate or higher
|
| 214 |
+
filtered = [r for r in results if r['impact'] in ['HIGH', 'MODERATE']]
|
| 215 |
+
print(f"\nVariants with MODERATE or HIGH impact: {len(filtered)}")
|
| 216 |
+
|
| 217 |
+
# Write CSV
|
| 218 |
+
output_csv = os.path.join(run_dir, "variants_shared.csv")
|
| 219 |
+
with open(output_csv, 'w', newline='') as f:
|
| 220 |
+
writer = csv.DictWriter(f, fieldnames=['chrom','pos','ref','alt','gene','impact','effect','status'])
|
| 221 |
+
writer.writeheader()
|
| 222 |
+
for r in filtered:
|
| 223 |
+
writer.writerow(r)
|
| 224 |
+
|
| 225 |
+
print(f"Written {len(filtered)} variants to {output_csv}")
|
| 226 |
+
|
| 227 |
+
# Write gene annotations
|
| 228 |
+
gene_csv = os.path.join(run_dir, "gene_annotations.csv")
|
| 229 |
+
with open(gene_csv, 'w', newline='') as f:
|
| 230 |
+
writer = csv.DictWriter(f, fieldnames=['chrom','pos','ref','alt','gene','impact','effect'])
|
| 231 |
+
writer.writeheader()
|
| 232 |
+
for r in gene_annotations:
|
| 233 |
+
writer.writerow(r)
|
| 234 |
+
|
| 235 |
+
print(f"Written {len(gene_annotations)} annotations to {gene_csv}")
|
| 236 |
+
|
| 237 |
+
# Show results
|
| 238 |
+
print("\n=== RESULT SUMMARY ===")
|
| 239 |
+
print(f"Total shared new variants: {len(new_variants)}")
|
| 240 |
+
print(f"MODERATE/HIGH impact: {len(filtered)}")
|
| 241 |
+
print(f"LOW/MODIFIER impact: {len(results) - len(filtered)}")
|
| 242 |
+
print("\nModerate+ impact variants:")
|
| 243 |
+
for r in filtered:
|
| 244 |
+
print(f" {r['chrom']}:{r['pos']} {r['ref']}>{r['alt']} gene={r['gene']} impact={r['impact']} effect={r['effect']}")
|
experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/ecoli_reference.amb
ADDED
|
@@ -0,0 +1 @@
|
|
|
|
|
|
|
| 1 |
+
4641652 1 0
|
experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/ecoli_reference.ann
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
4641652 1 11
|
| 2 |
+
0 NC_000913.3 Escherichia coli str. K-12 substr. MG1655, complete genome
|
| 3 |
+
0 4641652 0
|
experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/evol1.raw.vcf
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/evol1.sorted.bam.bai
ADDED
|
Binary file (34.1 kB). View file
|
|
|
experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/evol2.raw.vcf
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/evol2.sorted.bam.bai
ADDED
|
Binary file (33.8 kB). View file
|
|
|
experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/execution_log.json
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/execution_log.txt
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/final_answer.txt
ADDED
|
@@ -0,0 +1,36 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
1. [✓] Explore the input data directory (completed)
|
| 2 |
+
2. [✓] Check for available E. coli reference genomes (completed - found NC_000913.3 MG1655)
|
| 3 |
+
3. [✓] Assemble ancestor genome as reference using SPAdes (completed - 304 contigs, 4.55 Mb)
|
| 4 |
+
4. [✓] Annotate reference with Prokka (completed - 4194 CDS features identified)
|
| 5 |
+
5. [✓] Index the reference genome (BWA) (completed)
|
| 6 |
+
6. [✓] Align ancestor reads to reference (completed)
|
| 7 |
+
7. [✓] Align evolved line 1 reads to reference (completed)
|
| 8 |
+
8. [✓] Align evolved line 2 reads to reference (completed)
|
| 9 |
+
9. [✓] Call variants for each sample (FreeBayes - 707 ancestor, 461 evol1, 472 evol2)
|
| 10 |
+
10. [✓] Find shared variants between both evolved lines (266 shared, 143 novel)
|
| 11 |
+
11. [✓] Annotate variants using Prokka GFF and reference sequence
|
| 12 |
+
12. [✓] Filter for MODERATE or HIGH impact (57 variants of 143 total)
|
| 13 |
+
13. [✓] Output results in required CSV format
|
| 14 |
+
|
| 15 |
+
## Final Summary
|
| 16 |
+
|
| 17 |
+
**Task:** Experimental Evolution Variant Calling (E. coli)
|
| 18 |
+
|
| 19 |
+
**Pipeline executed:**
|
| 20 |
+
1. **Assembly:** SPAdes (isolate mode) assembled ancestor reads into 304 contigs (4.55 Mb total)
|
| 21 |
+
2. **Annotation:** Prokka identified 4,194 CDS features on the assembled reference
|
| 22 |
+
3. **Alignment:** BWA-MEM aligned ancestor, evol1, and evol2 paired-end reads to the assembled reference
|
| 23 |
+
4. **Variant Calling:** FreeBayes called 707 (ancestor), 461 (evol1), and 472 (evol2) variants
|
| 24 |
+
5. **Shared variant identification:** 143 variants shared by both evolved lines but absent in ancestor
|
| 25 |
+
6. **Impact annotation:** Custom Python annotation using GFF CDS coordinates and codon translation
|
| 26 |
+
|
| 27 |
+
**Results:**
|
| 28 |
+
- **variants_shared.csv**: 57 variants with MODERATE (53) or HIGH (4) impact shared by both evolved lines
|
| 29 |
+
- 4 HIGH impact variants: stop_lost (ACJFFICI_01666), frameshift_variant (malT_2, dcuS_1), stop_gained (yjjW)
|
| 30 |
+
- **gene_annotations.csv**: 126 total annotated variants (all impacts)
|
| 31 |
+
|
| 32 |
+
**Output files saved to:**
|
| 33 |
+
- `/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/variants_shared.csv`
|
| 34 |
+
- `/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/gene_annotations.csv`
|
| 35 |
+
|
| 36 |
+
<solution>Both files have been successfully generated and saved to the run directory. The variants_shared.csv contains 57 variants (MODERATE or HIGH impact) shared by both evolved lineages but absent in the ancestor, formatted with the required columns: CHROM, POS, REF, ALT, GENE, IMPACT, EFFECT, STATUS. The gene_annotations.csv contains all 126 annotated variants.</solution>
|
experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/output_validation.json
ADDED
|
@@ -0,0 +1,24 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"postprocess": [
|
| 3 |
+
{
|
| 4 |
+
"file": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/variants_shared.csv",
|
| 5 |
+
"actions": []
|
| 6 |
+
},
|
| 7 |
+
{
|
| 8 |
+
"file": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/gene_annotations.csv",
|
| 9 |
+
"actions": []
|
| 10 |
+
}
|
| 11 |
+
],
|
| 12 |
+
"outputs": [
|
| 13 |
+
{
|
| 14 |
+
"path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/variants_shared.csv",
|
| 15 |
+
"exists": true,
|
| 16 |
+
"size_bytes": 4978
|
| 17 |
+
},
|
| 18 |
+
{
|
| 19 |
+
"path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/gene_annotations.csv",
|
| 20 |
+
"exists": true,
|
| 21 |
+
"size_bytes": 10127
|
| 22 |
+
}
|
| 23 |
+
]
|
| 24 |
+
}
|
experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/run_summary.json
ADDED
|
@@ -0,0 +1,22 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"task_id": "evolution",
|
| 3 |
+
"run_dir": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912",
|
| 4 |
+
"outputs": [
|
| 5 |
+
{
|
| 6 |
+
"path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/variants_shared.csv",
|
| 7 |
+
"exists": true,
|
| 8 |
+
"size_bytes": 4978
|
| 9 |
+
},
|
| 10 |
+
{
|
| 11 |
+
"path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/gene_annotations.csv",
|
| 12 |
+
"exists": true,
|
| 13 |
+
"size_bytes": 10127
|
| 14 |
+
}
|
| 15 |
+
],
|
| 16 |
+
"planning_latency_seconds": 69.9531177021563,
|
| 17 |
+
"total_runtime_seconds": 1399.4747738316655,
|
| 18 |
+
"final_answer_path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/final_answer.txt",
|
| 19 |
+
"metadata_path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/run_metadata.json",
|
| 20 |
+
"retrieval_plan_path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/retrieval_plan.json",
|
| 21 |
+
"output_validation_path": "/225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/output_validation.json"
|
| 22 |
+
}
|
experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/task_query.txt
ADDED
|
@@ -0,0 +1,47 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
You are running a bioagent-bench task with local files already prepared.
|
| 2 |
+
|
| 3 |
+
Task ID: evolution
|
| 4 |
+
Task name: Experimental Evolution Variant Calling (E. coli)
|
| 5 |
+
Benchmark prompt:
|
| 6 |
+
Identify and annotate genome variants in two evolved lines relative to an ancestor lines of E. coli; report only variants shared by both evolved lines of moderate or higher predicted severity. The output should be a CSV file with the following columns: 'chrom','pos','ref','alt','gene','impact','effect',status'.<example>CHROM,POS,REF,ALT,GENE,IMPACT,EFFECT,STATUS
|
| 7 |
+
NODE_4_length_102007_cov_6.351643,6352,T,C,ICCIAKIK_00327,MODERATE,missense_variant,shared</example>
|
| 8 |
+
Data background:
|
| 9 |
+
The experiment follows a similar strategy as in what is called an experimental evolution experiment. The final aim is to identify the genome variations in evolved lines of E. coli. The data is composed of a single ancestor line and two evolved lines. The data is from a paired-end sequencing run data from an Illumina HiSeq. This data has been post-processed in two ways already. All sequences that were identified as belonging to the PhiX genome have been removed. Illumina adapters have been removed as well already.
|
| 10 |
+
|
| 11 |
+
Constraints:
|
| 12 |
+
1. Use only the benchmark inputs and references explicitly listed below.
|
| 13 |
+
2. Save the required final deliverables exactly to the paths listed below.
|
| 14 |
+
3. Save all intermediate scripts, logs, and scratch outputs inside this run directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912
|
| 15 |
+
4. Keep final deliverables in the same schema/format requested by the benchmark prompt.
|
| 16 |
+
5. Return a concise final summary after writing the required files.
|
| 17 |
+
|
| 18 |
+
Task-specific instruction:
|
| 19 |
+
Save variants_shared.csv and, if gene-level annotations are generated, gene_annotations.csv in the run directory.
|
| 20 |
+
|
| 21 |
+
Benchmark data policy:
|
| 22 |
+
- Allowed input data directory: /225040511/project/bioagent-bench/dataset/evolution/data
|
| 23 |
+
- Allowed reference directory: <none>
|
| 24 |
+
- Allowed scratch/output directory: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912
|
| 25 |
+
- Forbidden truth/results directory: /225040511/project/bioagent-bench/dataset/evolution/results
|
| 26 |
+
- Forbidden sibling benchmark task directories: /225040511/project/bioagent-bench/dataset/<any task other than evolution>
|
| 27 |
+
- Do not inspect previous bioagent-bench-runs or sibling task outputs as data sources.
|
| 28 |
+
- Do not download external databases or install new packages during the benchmark run.
|
| 29 |
+
|
| 30 |
+
Input data directory:
|
| 31 |
+
/225040511/project/bioagent-bench/dataset/evolution/data
|
| 32 |
+
Visible input files:
|
| 33 |
+
- anc_R1.fastq.gz
|
| 34 |
+
- anc_R2.fastq.gz
|
| 35 |
+
- evol1_R1.fastq.gz
|
| 36 |
+
- evol1_R2.fastq.gz
|
| 37 |
+
- evol2_R1.fastq.gz
|
| 38 |
+
- evol2_R2.fastq.gz
|
| 39 |
+
|
| 40 |
+
Reference data directory:
|
| 41 |
+
<none>
|
| 42 |
+
Visible reference files:
|
| 43 |
+
- <none>
|
| 44 |
+
|
| 45 |
+
Required final output paths:
|
| 46 |
+
- variants_shared.csv: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/variants_shared.csv
|
| 47 |
+
- gene_annotations.csv: /225040511/project/Biomni/experiments/bioagent_bench/runs/scale_1000/evolution_20260515_145912/gene_annotations.csv
|