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  1. .gitattributes +3 -0
  2. data/cBioPortal/crc_hta11_htan_2021/LICENSE +1 -0
  3. data/cBioPortal/crc_hta11_htan_2021/Readme.md +30 -0
  4. data/cBioPortal/crc_hta11_htan_2021/case_lists/cases_RNA_Seq_mRNA.txt +6 -0
  5. data/cBioPortal/crc_hta11_htan_2021/case_lists/cases_all.txt +6 -0
  6. data/cBioPortal/crc_hta11_htan_2021/case_lists/cases_sequenced.txt +6 -0
  7. data/cBioPortal/crc_hta11_htan_2021/data_absolute_counts.txt +17 -0
  8. data/cBioPortal/crc_hta11_htan_2021/data_clinical_patient.txt +57 -0
  9. data/cBioPortal/crc_hta11_htan_2021/data_clinical_sample.txt +66 -0
  10. data/cBioPortal/crc_hta11_htan_2021/data_gene_panel_matrix.txt +62 -0
  11. data/cBioPortal/crc_hta11_htan_2021/data_mutations.txt +3 -0
  12. data/cBioPortal/crc_hta11_htan_2021/data_pseudo_bulk_rna_seq_expression.txt +3 -0
  13. data/cBioPortal/crc_hta11_htan_2021/data_pseudo_bulk_rna_seq_expression_zscores_ref_all_samples.txt +3 -0
  14. data/cBioPortal/crc_hta11_htan_2021/data_relative_fraction.txt +17 -0
  15. data/cBioPortal/crc_hta11_htan_2021/data_resource_definition.txt +3 -0
  16. data/cBioPortal/crc_hta11_htan_2021/data_resource_sample.txt +98 -0
  17. data/cBioPortal/crc_hta11_htan_2021/meta_absolute_counts.txt +12 -0
  18. data/cBioPortal/crc_hta11_htan_2021/meta_clinical_patient.txt +4 -0
  19. data/cBioPortal/crc_hta11_htan_2021/meta_clinical_sample.txt +4 -0
  20. data/cBioPortal/crc_hta11_htan_2021/meta_gene_panel_matrix.txt +4 -0
  21. data/cBioPortal/crc_hta11_htan_2021/meta_mutations.txt +8 -0
  22. data/cBioPortal/crc_hta11_htan_2021/meta_pseudo_bulk_rna_seq_expression.txt +8 -0
  23. data/cBioPortal/crc_hta11_htan_2021/meta_pseudo_bulk_rna_seq_expression_zscores_ref_all_samples.txt +8 -0
  24. data/cBioPortal/crc_hta11_htan_2021/meta_relative_fraction.txt +12 -0
  25. data/cBioPortal/crc_hta11_htan_2021/meta_resource_definition.txt +3 -0
  26. data/cBioPortal/crc_hta11_htan_2021/meta_resource_sample.txt +3 -0
  27. data/cBioPortal/crc_hta11_htan_2021/meta_study.txt +6 -0
.gitattributes CHANGED
@@ -945,3 +945,6 @@ data/cBioPortal/prad_fhcrc/data_log2_cna.txt filter=lfs diff=lfs merge=lfs -text
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  data/cBioPortal/prad_fhcrc/data_mrna_agilent_microarray.txt filter=lfs diff=lfs merge=lfs -text
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  data/cBioPortal/prad_fhcrc/data_mrna_agilent_microarray_zscores_ref_all_samples.txt filter=lfs diff=lfs merge=lfs -text
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  data/cBioPortal/prad_fhcrc/data_mrna_agilent_microarray_zscores_ref_diploid_samples.txt filter=lfs diff=lfs merge=lfs -text
 
 
 
 
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  data/cBioPortal/prad_fhcrc/data_mrna_agilent_microarray.txt filter=lfs diff=lfs merge=lfs -text
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  data/cBioPortal/prad_fhcrc/data_mrna_agilent_microarray_zscores_ref_all_samples.txt filter=lfs diff=lfs merge=lfs -text
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  data/cBioPortal/prad_fhcrc/data_mrna_agilent_microarray_zscores_ref_diploid_samples.txt filter=lfs diff=lfs merge=lfs -text
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+ data/cBioPortal/crc_hta11_htan_2021/data_mutations.txt filter=lfs diff=lfs merge=lfs -text
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+ data/cBioPortal/crc_hta11_htan_2021/data_pseudo_bulk_rna_seq_expression.txt filter=lfs diff=lfs merge=lfs -text
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+ data/cBioPortal/crc_hta11_htan_2021/data_pseudo_bulk_rna_seq_expression_zscores_ref_all_samples.txt filter=lfs diff=lfs merge=lfs -text
data/cBioPortal/crc_hta11_htan_2021/LICENSE ADDED
@@ -0,0 +1 @@
 
 
1
+ The data are available under the ODC Open Database License (ODbL)(http://opendatacommons.org/licenses/odbl/1.0/) (summary available here: http://www.opendatacommons.org/licenses/odbl/1-0/summary/): you are free to share and modify the data so long as you attribute any public use of the database, or works produced from the database; keep the resulting data-sets open; and offer your shared or adapted version of the data-set under the same ODbL license.
data/cBioPortal/crc_hta11_htan_2021/Readme.md ADDED
@@ -0,0 +1,30 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ # Curation and transformation of Pre-cancer HTAN CRC Vanderbilt Dataset:
2
+
3
+ ## Data collection:
4
+ - Data Source: [Data on HTAN Portal](https://data.humantumoratlas.org/publications/vanderbilt_crc_chen_2021?tab=abstract)
5
+ - Reference publication: [PubMed Reference](https://pubmed.ncbi.nlm.nih.gov/34910928/)
6
+ - Reference genome used: GRCh37 for WXS and GRCh38 for scRNA-seq
7
+
8
+ ## Sample size selection
9
+ - Discovery & Validation set samples were used to generate the study (61 polyps). 30 samples were whole exome sequenced. 55 samples went though scRNA-seq exp analysis.
10
+ - Two patients (`HTA11_3918 and HTA11_4781`) were not listed in the supplementary clinical tables but were included in the Oncoplot analysis (Figure 1). They have been added to the cohort to match the oncoplot.
11
+
12
+ ## Clinical data
13
+ - Patient-Level Data: `Table S1`, `Participants` tab in HTAN Portal
14
+ - Sample-Level Data:`Table S1`, `Biospecimens` tab in HTAN Portal
15
+
16
+ ## Mutation data
17
+ - The Level 3 Bulk DNA filtered data files were obtained from the Vanderbilt team.
18
+ - Variants were annotated using Genome Nexus.
19
+
20
+ ## scRNA-seq data
21
+ - The Discovery, Validation set h5ad files for both epithelial and non-epithelial cells were used from [cellxgene](https://cellxgene.cziscience.com/collections/a48f5033-3438-4550-8574-cdff3263fdfd)
22
+ - Files used: `Discovery (DIS) set of human colorectal tumor: Epithelial` && `Validation (Val) set of human colorectal tumor: Epithelial` && `VAL and DIS datasets: Non-Epithelial`
23
+ - The absolute and relative cell frequencies in Generic Assay format were calculated
24
+ - The pseudo bulk RNA expression counts per sample was calculated from scRNA-seq by averaging the values across the cells.
25
+ - The script to generate the absolute, relative cell freq and pseudo bulk RNA-seq data from h5ad files : https://gist.github.com/rmadupuri/447b5689b256ccc4880aa26fb91b72ff
26
+ - The pseudo bulk RNA expression data was log transformed and zscores were calculated.
27
+
28
+ ## Imaging data
29
+ - H&E data was available for 26 samples: `H&E` tab
30
+ - MxIF images were available for 25 samples: `MxIF` tab. Multiple images were available per sample and as we do not support this, the images were split to multiple tabs for now as MxIF Image 1, 2, 3..
data/cBioPortal/crc_hta11_htan_2021/case_lists/cases_RNA_Seq_mRNA.txt ADDED
@@ -0,0 +1,6 @@
 
 
 
 
 
 
 
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+ cancer_study_identifier: crc_hta11_htan_2021
2
+ stable_id: crc_hta11_htan_2021_rna_seq_mrna
3
+ case_list_name: Samples with mRNA data (RNA Seq)
4
+ case_list_description: Samples with mRNA expression data (55 samples)
5
+ case_list_category: all_cases_with_mrna_rnaseq_data
6
+ case_list_ids: HTA11_3331_2000001011 HTA11_392_3000011011 HTA11_7179_2000001011 HTA11_3361_2000001011 HTA11_1391_2000001011 HTA11_866_3004761011 HTA11_5216_2000001011 HTA11_2487_2000001011 HTA11_6801_2000001021 HTA11_9408_2000001011 HTA11_347_2000001011 HTA11_6134_2000001011 HTA11_6801_2000001011 HTA11_11156_2000001021 HTA11_6182_2000001011 HTA11_10167_2000001011 HTA11_7469_2000001011 HTA11_7029_2000001011 HTA11_10711_2000001011 HTA11_7956_2000001011 HTA11_2992_2000001011 HTA11_6818_2000001011 HTA11_3410_2000001011 HTA11_10623_2000001011 HTA11_8622_2000001011 HTA11_411_2000001011 HTA11_546_2000001011 HTA11_7696_3000711011 HTA11_78_2000001011 HTA11_696_2000001011 HTA11_2951_2000001011 HTA11_2112_2000001011 HTA11_866_2000001011 HTA11_6298_2000001011 HTA11_5363_2000001011 HTA11_7128_2000001011 HTA11_9341_2000001011 HTA11_6147_2000001011 HTA11_8622_2000001021 HTA11_104_2000001011 HTA11_11156_2000001011 HTA11_7663_2000001011 HTA11_8099_2000001011 HTA11_5994_2000001011 HTA11_2235_2000001011 HTA11_83_2000001011 HTA11_8920_2000001011 HTA11_6025_2000001011 HTA11_6818_2000001021 HTA11_5212_2000001011 HTA11_6310_2000001011 HTA11_1938_2000001011 HTA11_4255_2000001011 HTA11_11167_2000001011 HTA11_7862_2000001011
data/cBioPortal/crc_hta11_htan_2021/case_lists/cases_all.txt ADDED
@@ -0,0 +1,6 @@
 
 
 
 
 
 
 
1
+ cancer_study_identifier: crc_hta11_htan_2021
2
+ stable_id: crc_hta11_htan_2021_all
3
+ case_list_name: All samples
4
+ case_list_description: All samples (61 samples)
5
+ case_list_category: all_cases_in_study
6
+ case_list_ids: HTA11_3331_2000001011 HTA11_392_3000011011 HTA11_7179_2000001011 HTA11_1391_2000001011 HTA11_6801_2000001021 HTA11_9408_2000001011 HTA11_7663_2000009901 HTA11_11156_2000001021 HTA11_10167_2000001011 HTA11_8622_2000001011 HTA11_7029_2000001011 HTA11_10711_2000001011 HTA11_7956_2000001011 HTA11_7862_2000009901 HTA11_6818_2000001011 HTA11_3410_2000001011 HTA11_10623_2000001011 HTA11_78_2000001011 HTA11_8099_2000001011 HTA11_2951_2000001011 HTA11_9341_2000001011 HTA11_8622_2000001021 HTA11_7128_2000001011 HTA11_7696_3000711011 HTA11_2235_2000001011 HTA11_9341_2000009901 HTA11_2487_2000001011 HTA11_8920_2000001011 HTA11_6025_2000001011 HTA11_10167_2000009901 HTA11_5212_2000001011 HTA11_2112_2000001011 HTA11_11167_2000001011 HTA11_7862_2000001011 HTA11_6134_2000001011 HTA11_3361_2000001011 HTA11_866_3004761011 HTA11_5216_2000001011 HTA11_347_2000001011 HTA11_6801_2000001011 HTA11_6182_2000001011 HTA11_7469_2000001011 HTA11_4781_2000001011 HTA11_696_2000001011 HTA11_411_2000001011 HTA11_546_2000001011 HTA11_6298_2000001011 HTA11_104_2000001011 HTA11_866_2000001011 HTA11_7663_2000001011 HTA11_5363_2000001011 HTA11_6147_2000001011 HTA11_11156_2000001011 HTA11_2992_2000001011 HTA11_5994_2000001011 HTA11_83_2000001011 HTA11_6818_2000001021 HTA11_3918_2000001011 HTA11_6310_2000001011 HTA11_1938_2000001011 HTA11_4255_2000001011
data/cBioPortal/crc_hta11_htan_2021/case_lists/cases_sequenced.txt ADDED
@@ -0,0 +1,6 @@
 
 
 
 
 
 
 
1
+ cancer_study_identifier: crc_hta11_htan_2021
2
+ stable_id: crc_hta11_htan_2021_sequenced
3
+ case_list_name: Samples with mutation data
4
+ case_list_description: Samples with mutation data (30 samples)
5
+ case_list_category: all_cases_with_mutation_data
6
+ case_list_ids: HTA11_6134_2000001011 HTA11_1391_2000001011 HTA11_866_3004761011 HTA11_5216_2000001011 HTA11_347_2000001011 HTA11_6801_2000001011 HTA11_7663_2000009901 HTA11_8622_2000001011 HTA11_10711_2000001011 HTA11_7862_2000009901 HTA11_10623_2000001011 HTA11_696_2000001011 HTA11_866_2000001011 HTA11_5363_2000001011 HTA11_6147_2000001011 HTA11_8622_2000001021 HTA11_7696_3000711011 HTA11_4781_2000001011 HTA11_2235_2000001011 HTA11_9341_2000009901 HTA11_2487_2000001011 HTA11_8920_2000001011 HTA11_6025_2000001011 HTA11_10167_2000009901 HTA11_3918_2000001011 HTA11_5212_2000001011 HTA11_3331_2000001011 HTA11_6310_2000001011 HTA11_1938_2000001011 HTA11_4255_2000001011
data/cBioPortal/crc_hta11_htan_2021/data_absolute_counts.txt ADDED
@@ -0,0 +1,17 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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+ ENTITY_STABLE_ID NAME ONTOLOGY_ID HTA11_78_2000001011 HTA11_83_2000001011 HTA11_104_2000001011 HTA11_347_2000001011 HTA11_392_3000011011 HTA11_411_2000001011 HTA11_546_2000001011 HTA11_696_2000001011 HTA11_866_2000001011 HTA11_866_3004761011 HTA11_1391_2000001011 HTA11_1938_2000001011 HTA11_2112_2000001011 HTA11_2235_2000001011 HTA11_2487_2000001011 HTA11_2951_2000001011 HTA11_2992_2000001011 HTA11_3331_2000001011 HTA11_3361_2000001011 HTA11_3410_2000001011 HTA11_4255_2000001011 HTA11_5212_2000001011 HTA11_5216_2000001011 HTA11_5363_2000001011 HTA11_5994_2000001011 HTA11_6025_2000001011 HTA11_6134_2000001011 HTA11_6147_2000001011 HTA11_6182_2000001011 HTA11_6298_2000001011 HTA11_6310_2000001011 HTA11_6801_2000001011 HTA11_6801_2000001021 HTA11_6818_2000001011 HTA11_6818_2000001021 HTA11_7029_2000001011 HTA11_7128_2000001011 HTA11_7179_2000001011 HTA11_7469_2000001011 HTA11_7696_3000711011 HTA11_7956_2000001011 HTA11_8099_2000001011 HTA11_8622_2000001011 HTA11_8622_2000001021 HTA11_8920_2000001011 HTA11_9408_2000001011 HTA11_10623_2000001011 HTA11_10711_2000001011 HTA11_11156_2000001011 HTA11_11156_2000001021 HTA11_11167_2000001011 HTA11_7663_2000001011 HTA11_7862_2000001011 HTA11_9341_2000001011 HTA11_10167_2000001011
2
+ ABS Absorptive Cell CL_0000212 337 927 46 1427 13 530 523 1482 1281 38 56 200 498 106 1977 250 167 248 1679 206 514 500 333 256 743 143 165 48 22 123 215 497 545 131 105 28 29 131 1189 109 1046 247 171 266 267 36 574 139 73 34 313 1555 405 390 382
3
+ ASC Neoplastic Cell CL_0001063 587 59 4 8 70 46 271 738 624 347 693 1671 11 196 180 287 11 9 553 822 75 5 25 7 190 20 38 20 275 235 17 15 65 679 1281 428 95 68 1 741 6 15 54 107 8 82 49 219 91 12 103 42 4 12 1
4
+ B B Cell CL_0000236 1 0 0 8 0 0 0 0 1 1 3 3 0 0 0 2 0 2 4 0 9 0 0 0 0 0 0 0 0 0 5 0 0 6 2 0 0 0 1 4 0 0 18 2 0 0 0 2 0 1 0 15 0 30 6
5
+ CT Intestinal Epithelial Cell CL_0002563 3 32 0 122 0 25 10 28 31 0 1 1 11 2 102 2 24 15 13 0 18 28 9 15 25 1 7 1 0 3 13 29 28 0 0 0 0 8 88 1 48 39 4 9 16 0 12 0 1 1 1 30 54 13 1
6
+ EE Intestinal Enteroendocrine Cell CL_1001516 4 4 0 18 3 50 2 11 12 0 3 2 14 0 7 1 5 3 12 1 8 9 2 1 8 1 21 4 0 3 3 8 20 0 0 0 1 3 7 0 12 15 9 15 13 3 5 0 2 0 1 8 14 9 4
7
+ END Endocytes CL_0000115 0 4 0 2 0 2 0 1 0 7 1 2 1 0 1 1 1 0 8 0 8 0 0 0 0 0 4 2 0 0 2 2 8 7 3 0 0 0 0 13 0 0 4 8 0 0 1 2 0 0 0 1 0 4 0
8
+ FIB Fibroblasts CL_0000057 0 2 0 3 0 1 0 0 0 1 0 8 0 0 0 0 0 0 9 1 0 0 0 0 0 0 4 1 0 0 7 2 2 5 3 0 2 0 0 11 0 0 3 1 0 0 21 1 0 2 2 19 17 1 2
9
+ GOB Goblet Cell CL_0000160 518 190 2 42 69 298 181 905 595 389 61 89 484 40 457 147 18 9 821 493 79 2 76 7 50 12 28 6 94 144 51 186 247 285 84 163 23 95 4 179 90 94 65 117 107 4 149 54 76 12 100 124 176 21 54
10
+ MAS Mast Cell CL_0000097 3 8 1 7 0 5 0 17 1 2 1 7 0 0 7 15 0 5 55 7 8 0 0 0 0 1 3 0 0 0 2 0 4 6 2 0 0 0 3 5 0 0 24 14 4 1 2 0 2 0 0 39 2 5 0
11
+ MYE Myleoid Cell CL_0000763 0 4 2 3 0 3 0 2 3 10 3 12 0 1 3 4 0 6 17 2 5 0 0 0 0 0 3 2 0 0 3 3 8 7 13 0 0 0 0 16 0 0 23 11 2 0 1 4 4 1 5 58 17 4 1
12
+ PLA Plasma Cell CL_0000786 34 78 4 67 0 5 1 13 16 6 5 44 1 0 7 114 0 27 147 25 37 0 0 0 0 3 18 0 1 0 7 3 3 23 53 0 2 0 12 11 0 0 109 17 6 0 11 3 2 3 0 403 9 18 10
13
+ SSC Abnormal Cell CL_0001061 0 1 0 1 65 291 1 32 0 10 16 11 158 2 2280 7 0 94 22 6 469 3 0 8 266 0 162 43 3 7 112 342 16 3 12 18 0 2 1 28 0 198 648 876 34 1 0 0 6 0 13 4 0 27 18
14
+ STM Intestinal Crypt Stem Cell of Colon CL_0009043 192 82 19 250 0 19 2 3 23 30 1 21 0 4 19 0 15 4 0 11 32 3 6 2 0 5 0 6 2 43 11 54 14 6 5 2 0 1 29 25 159 36 9 38 19 1 38 10 2 2 4 83 102 9 31
15
+ T T Cell CL_0000084 1 79 3 68 0 76 1 15 48 12 96 154 31 2 63 43 0 204 78 14 147 0 0 0 0 3 88 11 0 0 15 75 39 22 47 0 1 0 71 41 0 0 168 65 24 12 119 52 4 0 7 117 24 50 30
16
+ TAC Transit Amplifying Cell CL_0009010 115 119 5 91 12 67 97 332 71 107 152 165 42 61 199 69 21 28 186 182 44 3 36 14 68 13 66 19 25 70 51 127 79 33 35 41 12 22 31 76 130 43 17 58 38 13 53 50 34 15 113 176 98 43 46
17
+ TUF Tuft Cell CL_0002204 17 17 3 7 12 2 11 33 33 11 9 18 6 2 44 7 0 6 14 14 34 3 7 0 14 8 0 3 1 50 4 6 0 5 1 4 3 4 6 29 24 8 8 17 4 0 31 1 1 0 7 26 4 25 6
data/cBioPortal/crc_hta11_htan_2021/data_clinical_patient.txt ADDED
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1
+ #Patient Identifier Age Sex Race Category Polyps of the Colon or Rectum? Atlas Name
2
+ #Identifier to uniquely specify a patient. Patient Age Sex The text for reporting information about race. Have you ever been told by a Doctor that you have polyps of the Colon or Rectum? Atlas Name
3
+ #STRING NUMBER STRING STRING STRING STRING
4
+ #1 5 5 3 1 6
5
+ PATIENT_ID AGE SEX RACE POLYP_OF_COLON_OR_RECTUM ATLAS_NAME
6
+ HTA11_78 67 Male White No HTAN Vanderbilt
7
+ HTA11_347 60 Female Other Not sure HTAN Vanderbilt
8
+ HTA11_546 73 Male White Yes HTAN Vanderbilt
9
+ HTA11_104 54 Male White No HTAN Vanderbilt
10
+ HTA11_392 62 Female White Yes HTAN Vanderbilt
11
+ HTA11_696 50 Male White No HTAN Vanderbilt
12
+ HTA11_1391 58 Male White Yes HTAN Vanderbilt
13
+ HTA11_2951 50 Female Black or African American No HTAN Vanderbilt
14
+ HTA11_3361 59 Male White Yes HTAN Vanderbilt
15
+ HTA11_3410 70 Male White No HTAN Vanderbilt
16
+ HTA11_2235 62 Female Black or African American No HTAN Vanderbilt
17
+ HTA11_5212 50 Male Black or African American No HTAN Vanderbilt
18
+ HTA11_6025 68 Male White Yes HTAN Vanderbilt
19
+ HTA11_866 71 Male White Yes HTAN Vanderbilt
20
+ HTA11_1938 53 Female White Yes HTAN Vanderbilt
21
+ HTA11_2487 65 Female White Yes HTAN Vanderbilt
22
+ HTA11_3331 68 Male White Yes HTAN Vanderbilt
23
+ HTA11_5363 50 Female White No HTAN Vanderbilt
24
+ HTA11_83 64 Male Black or African American Yes HTAN Vanderbilt
25
+ HTA11_2112 72 Female White No HTAN Vanderbilt
26
+ HTA11_5216 64 Female Black or African American No HTAN Vanderbilt
27
+ HTA11_6310 62 Male White Yes HTAN Vanderbilt
28
+ HTA11_411 50 Female White No HTAN Vanderbilt
29
+ HTA11_2992 73 Male White No HTAN Vanderbilt
30
+ HTA11_5994 67 Male White Yes HTAN Vanderbilt
31
+ HTA11_6134 54 Male White No HTAN Vanderbilt
32
+ HTA11_6147 50 Male Unknown No HTAN Vanderbilt
33
+ HTA11_3918 58 Female White Yes HTAN Vanderbilt
34
+ HTA11_4255 57 Male White No HTAN Vanderbilt
35
+ HTA11_4781 Male Black or African American HTAN Vanderbilt
36
+ HTA11_6182 52 Male White No HTAN Vanderbilt
37
+ HTA11_6298 72 Male White No HTAN Vanderbilt
38
+ HTA11_6801 64 Male White Yes HTAN Vanderbilt
39
+ HTA11_6818 63 Male Not stated No HTAN Vanderbilt
40
+ HTA11_7029 67 Female White Yes HTAN Vanderbilt
41
+ HTA11_7128 53 Female Black or African American Yes HTAN Vanderbilt
42
+ HTA11_7179 64 Male Not stated Yes HTAN Vanderbilt
43
+ HTA11_7469 46 Female Black or African American No HTAN Vanderbilt
44
+ HTA11_7663 62 Male Black or African American Yes HTAN Vanderbilt
45
+ HTA11_7696 68 Male White Yes HTAN Vanderbilt
46
+ HTA11_7862 52 Male Black or African American No HTAN Vanderbilt
47
+ HTA11_7956 56 Male White Yes HTAN Vanderbilt
48
+ HTA11_8099 70 Female White Yes HTAN Vanderbilt
49
+ HTA11_8622 66 Female White Yes HTAN Vanderbilt
50
+ HTA11_8920 51 Female White Yes HTAN Vanderbilt
51
+ HTA11_9341 51 Male White Not stated HTAN Vanderbilt
52
+ HTA11_9408 74 Male White No HTAN Vanderbilt
53
+ HTA11_10167 52 Male White No HTAN Vanderbilt
54
+ HTA11_10623 55 Male Black or African American Yes HTAN Vanderbilt
55
+ HTA11_10711 52 Female White No HTAN Vanderbilt
56
+ HTA11_11156 67 Female White Yes HTAN Vanderbilt
57
+ HTA11_11167 60 Female White No HTAN Vanderbilt
data/cBioPortal/crc_hta11_htan_2021/data_clinical_sample.txt ADDED
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1
+ #Patient Identifier Sample Identifier Tumor Tissue Type Polyp Type Polyp Subtype Hyperplastic Type Advanced Atypia Percent Adenoma Percent Normal Cells Percent Villous Component Polyp Dimension Polyp Shape Sample Size Invivo (cm) Side Segment Acquisition Method Type Preservation Method Cohort Somatic Status
2
+ #Identifier to uniquely specify a patient. A unique sample identifier. Tumor Tissue Type Polyp Type Polyp Subtype Hyperplastic Type Developed or Progressed State Atypia Proportion of Adenoma within the polyp Proportion of Normal cells within the polyp Villous Component within the polyp Polyp Dimension Polyp Shape Sample Size Invivo (cm) Location of polyp Location of polyp Acquisition Method Type Preservation Method Cohort Somatic Status
3
+ #STRING STRING STRING STRING STRING STRING STRING STRING STRING STRING STRING NUMBER STRING NUMBER STRING STRING STRING STRING STRING STRING
4
+ #1 1 6 6 6 5 5 5 3 3 3 3 3 3 4 4 1 1 1 1
5
+ PATIENT_ID SAMPLE_ID TISSUE_TYPE POLYP_TYPE POLYP_SUBTYPE HPTYPE ADVANCED ATYPIA PCAD PCNORMAL PCVILLOUS PDIM PSHAPE SAMPLE_SIZEINVIVO_CM SIDE SEGMENT ACQUISITION_METHOD PRESERVATION_METHOD COHORT SOMATIC_STATUS
6
+ HTA11_78 HTA11_78_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic Not Stated Not stated 1-25% >=31% 0% 1 Sessile 0.4 Distal Descending colon Biopsy Fresh Discovery Matched
7
+ HTA11_347 HTA11_347_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 1-25% >=31% 0% 0.8 Sessile 0.7 Distal Descending colon Biopsy Fresh Discovery Matched
8
+ HTA11_546 HTA11_546_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 100% 0% 0% 0.4 Sessile 0.6 Proximal Transverse colon Biopsy Fresh Discovery Matched
9
+ HTA11_104 HTA11_104_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 0.7 Not stated 0.6 Proximal Transverse colon Biopsy Fresh Discovery Matched
10
+ HTA11_392 HTA11_392_3000011011 Premalignant Unknown Unknown Not Stated No Low-grade dysplasia 76-99% >=31% 1-25% 0.6 Sessile 0.6 Proximal Cecum Biopsy Fresh Discovery Matched
11
+ HTA11_696 HTA11_696_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 26-50% >=31% 1-25% 0.4 Sessile 0.8 Distal Sigmoid colon Biopsy Fresh Discovery Matched
12
+ HTA11_1391 HTA11_1391_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 76-99% 21-30% 0% 0.3 Sessile 0.5 Proximal Ascending colon Biopsy Fresh Discovery Matched
13
+ HTA11_2951 HTA11_2951_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 76-99% 11-20% 1-25% 0.4 Sessile 0.8 Proximal Ascending colon Biopsy Fresh Discovery Matched
14
+ HTA11_3361 HTA11_3361_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 26-50% >=31% 0% 0.4 Sessile 0.5 Proximal Ascending colon Biopsy Fresh Discovery Matched
15
+ HTA11_3410 HTA11_3410_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 100% 0% 0% 0.2 Sessile 0.8 Proximal Transverse colon Biopsy Fresh Discovery Matched
16
+ HTA11_2235 HTA11_2235_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 76-99% 6-10% 0% 0.2 Sessile 0.5 Proximal Hepatic flexure Biopsy Fresh Discovery Matched
17
+ HTA11_5212 HTA11_5212_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 76-99% 3-5% 0% 0.4 Sessile 0.6 Distal Rectum Biopsy Fresh Discovery Matched
18
+ HTA11_6025 HTA11_6025_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 100% 0% 0% 0.4 Sessile 0.5 Proximal Ascending colon Biopsy Fresh Discovery Matched
19
+ HTA11_866 HTA11_866_2000001011 Premalignant AD Tubulovillous Adenoma Not Hyperplastic Yes Low-grade dysplasia 100% 0% 51-75% 0.5 Pedunculated 0.7 Distal Descending colon Biopsy Fresh Discovery Matched
20
+ HTA11_1938 HTA11_1938_2000001011 Premalignant AD Tubulovillous Adenoma Not Hyperplastic Yes High-grade dysplasia 76-99% 3-5% 26-50% 1.7 Sessile 2.5 Proximal Cecum Biopsy Fresh Discovery Matched
21
+ HTA11_2487 HTA11_2487_2000001011 Premalignant SER Sessile Serrated Lesion Not Hyperplastic Yes No dysplasia Not Stated Not stated Not Stated 1.2 Sessile 1.2 Proximal Ascending colon Biopsy Fresh Discovery Matched
22
+ HTA11_3331 HTA11_3331_2000001011 Premalignant SER Sessile Serrated Lesion Not Hyperplastic Yes No dysplasia Not Stated Not stated Not Stated 0.9 Sessile 1 Proximal Cecum Biopsy Fresh Discovery Matched
23
+ HTA11_5363 HTA11_5363_2000001011 Premalignant SER Sessile Serrated Lesion Not Hyperplastic No No dysplasia 100% 0% 0% 0.4 Sessile 0.8 Distal Sigmoid colon Biopsy Fresh Discovery Matched
24
+ HTA11_83 HTA11_83_2000001011 Atypia - hyperplasia SER Microvesicular Hyperplastic Polyp Microvesicular Not Stated No dysplasia 0% 0% 0.4 Sessile 0.5 Proximal Cecum Biopsy Fresh Discovery Matched
25
+ HTA11_2112 HTA11_2112_2000001011 Atypia - hyperplasia SER Hyperplastic Polyp Not Stated Not Stated No dysplasia 0% >=31% 0% 0.4 Sessile 0.8 Distal Sigmoid colon Biopsy Fresh Discovery Matched
26
+ HTA11_5216 HTA11_5216_2000001011 Atypia - hyperplasia SER Goblet cell-rich Hyperplastic Polyp Goblet-cell rich Not Stated No dysplasia 0% 0% 0% 0.6 Sessile 0.5 Distal Sigmoid colon Biopsy Fresh Discovery Matched
27
+ HTA11_6310 HTA11_6310_2000001011 Premalignant SER Microvesicular Hyperplastic Polyp Microvesicular Not Stated No dysplasia 0% 21-30% 0% 0.7 Sessile 0.6 Distal Descending colon Biopsy Fresh Discovery Matched
28
+ HTA11_411 HTA11_411_2000001011 Not Otherwise Specified SER Hyperplastic Polyp Not Stated Not Stated Not Stated Not Stated Not stated Not Stated Not Stated Distal Rectum Biopsy Fresh Discovery Matched
29
+ HTA11_2992 HTA11_2992_2000001011 Atypia - hyperplasia SER Microvesicular Hyperplastic Polyp Microvesicular Not Stated No dysplasia 0% 1-2% 0% 0.4 Sessile 0.5 Distal Sigmoid colon Biopsy Fresh Discovery Matched
30
+ HTA11_5994 HTA11_5994_2000001011 Not Otherwise Specified Unknown Unknown Not Stated Not Stated Not Stated Not Stated Not stated Not Stated Not Stated 0.6 Proximal Ascending colon Biopsy Fresh Discovery Matched
31
+ HTA11_6134 HTA11_6134_2000001011 Atypia - hyperplasia SER Goblet cell-rich Hyperplastic Polyp Goblet-cell rich Not Stated No dysplasia 0% 0% 0% 0.5 Sessile 0.5 Distal Sigmoid colon Biopsy Fresh Discovery Matched
32
+ HTA11_6147 HTA11_6147_2000001011 Atypia - hyperplasia SER Microvesicular Hyperplastic Polyp Microvesicular Not Stated No dysplasia 0% 3-5% 0% 0.3 Sessile 0.5 Distal Sigmoid colon Biopsy Fresh Discovery Matched
33
+ HTA11_866 HTA11_866_3004761011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 100% 0% 1-25% 0.4 Sessile 0.8 Distal Descending colon Biopsy Fresh Validation Matched
34
+ HTA11_3918 HTA11_3918_2000001011 Premalignant AD Tubular Adenoma Not Stated Not Stated Not Stated Not Stated Not stated Not Stated Not Stated 2 Proximal Ascending colon Biopsy Fresh Validation Matched
35
+ HTA11_4255 HTA11_4255_2000001011 Atypia - hyperplasia SER Microvesicular Hyperplastic Polyp Microvesicular Yes No dysplasia 0% >=31% 0% 0.3 Flat 1 Proximal Transverse colon Biopsy Fresh Validation Matched
36
+ HTA11_4781 HTA11_4781_2000001011 Premalignant AD Tubular Adenoma 0.5 Biopsy Fresh Validation Matched
37
+ HTA11_6182 HTA11_6182_2000001011 Premalignant AD Tubulovillous Adenoma Not Hyperplastic Yes Low-grade dysplasia 100% 0% 51-75% 0.4 Not stated 1.5 Distal Descending colon Biopsy Fresh Validation Matched
38
+ HTA11_6298 HTA11_6298_2000001011 Premalignant Unknown Unknown Not stated Not stated Not stated Not stated Not stated 0% 1.4 Sessile 0.8 Proximal Transverse colon Biopsy Fresh Validation Matched
39
+ HTA11_6801 HTA11_6801_2000001011 Premalignant SER Sessile Serrated Lesion Not Hyperplastic No No dysplasia 51-75% >=31% 0% 0.5 Sessile 0.5 Proximal Ascending colon Biopsy Fresh Validation Matched
40
+ HTA11_6801 HTA11_6801_2000001021 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 1-25% 0.7 Pedunculated 0.8 Distal Sigmoid colon Biopsy Fresh Validation Matched
41
+ HTA11_6818 HTA11_6818_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic Yes Low-grade dysplasia 76-99% 3-5% 0% 0.6 Pedunculated 1 Distal Descending colon Biopsy Fresh Validation Matched
42
+ HTA11_6818 HTA11_6818_2000001021 Premalignant AD Tubulovillous Adenoma Not Hyperplastic Yes High-grade dysplasia Not stated Not stated Not stated 2 Not stated 2.5 Proximal Ascending colon Biopsy Fresh Validation Matched
43
+ HTA11_7029 HTA11_7029_2000001011 Premalignant Unknown Unknown Not Hyperplastic No Low-grade dysplasia 100% 0% 1-25% 0.4 Sessile 0.8 Proximal Ascending colon Biopsy Fresh Validation Matched
44
+ HTA11_7128 HTA11_7128_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 76-99% 11-20% 1-25% 1 Pedunculated 0.8 Distal Rectum Biopsy Fresh Validation Matched
45
+ HTA11_7179 HTA11_7179_2000001011 Premalignant Unknown Unknown Not stated No Low-grade dysplasia 1-25% >=31% 1-25% 1.3 Sessile 0.6 Distal Descending colon Biopsy Fresh Validation Matched
46
+ HTA11_7469 HTA11_7469_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 26-50% >=31% 0% 0.2 Sessile 0.5 Proximal Transverse colon Biopsy Fresh Validation Matched
47
+ HTA11_7663 HTA11_7663_2000009901 Not Otherwise Specified SER Sessile Serrated Lesion Not Hyperplastic No No dysplasia 51-75% >=31% 0% 0.6 Flat 0.6 Proximal Cecum Other Acquisition Method Frozen Validation Matched
48
+ HTA11_7696 HTA11_7696_3000711011 Premalignant AD Tubular Adenoma Not Hyperplastic Yes Low-grade dysplasia 26-50% >=31% 1-25% 1.5 Not stated 1.5 Proximal Cecum Biopsy Snap Frozen Validation Matched
49
+ HTA11_7862 HTA11_7862_2000009901 Not Otherwise Specified AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 1-25% >=31% 0% 0.4 Sessile 0.7 Distal Sigmoid colon Other Acquisition Method Frozen Validation Matched
50
+ HTA11_7956 HTA11_7956_2000001011 Not Otherwise Specified Unknown Unknown Not stated Not stated Not stated Not stated Not stated 0% 0.4 Sessile 0.6 Proximal Ascending colon Biopsy Fresh Validation Matched
51
+ HTA11_8099 HTA11_8099_2000001011 Not Otherwise Specified Unknown Unknown Not stated Not stated Not stated Not stated Not stated 0% 0.4 Sessile 0.6 Proximal Transverse colon Biopsy Fresh Validation Matched
52
+ HTA11_8622 HTA11_8622_2000001011 Premalignant SER Sessile Serrated Lesion Not Hyperplastic Yes No dysplasia 76-99% 0% 1.2 Sessile 1.2 Proximal Ascending colon Biopsy Fresh Validation Matched
53
+ HTA11_8622 HTA11_8622_2000001021 Premalignant SER Sessile Serrated Lesion Not Hyperplastic No No dysplasia 76-99% 6-10% 0% 0.7 Sessile 0.8 Proximal Hepatic flexure Biopsy Fresh Validation Matched
54
+ HTA11_8920 HTA11_8920_2000001011 Atypia - hyperplasia SER Goblet cell-rich Hyperplastic Polyp Goblet-cell rich Yes No dysplasia 76-99% 21-30% 0% 0.3 Sessile 8.8 Distal Descending colon Biopsy Fresh Validation Matched
55
+ HTA11_9341 HTA11_9341_2000009901 Not Otherwise Specified SER Sessile Serrated Lesion Not Hyperplastic Yes No dysplasia 76-99% 6-10% 1-25% 0.8 Flat 1 Proximal Ascending colon Other Acquisition Method Frozen Validation Matched
56
+ HTA11_9408 HTA11_9408_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic Yes Low-grade dysplasia 100% 0% 0% 0.6 Sessile 1 Proximal Ascending colon Biopsy Fresh Validation Matched
57
+ HTA11_10167 HTA11_10167_2000009901 Not Otherwise Specified SER Sessile Serrated Lesion Not Hyperplastic No No dysplasia 100% 0% 1-25% 0.4 Sessile 0.5 Proximal Ascending colon Other Acquisition Method Frozen Validation Matched
58
+ HTA11_10623 HTA11_10623_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 1-25% >=31% 1-25% 0.4 Sessile 0.6 Proximal Hepatic flexure Biopsy Fresh Validation Matched
59
+ HTA11_10711 HTA11_10711_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 1-25% >=31% 0% 0.4 Sessile 0.7 Proximal Cecum Biopsy Fresh Validation Matched
60
+ HTA11_11156 HTA11_11156_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic Yes Low-grade dysplasia 76-99% 3-5% 0% 0.8 Sessile 1 Distal Sigmoid colon Biopsy Fresh Validation Matched
61
+ HTA11_11156 HTA11_11156_2000001021 Premalignant AD Tubular Adenoma Not Hyperplastic Yes Low-grade dysplasia 100% 0% 0% 0.5 Sessile 1 Proximal Cecum Biopsy Fresh Validation Matched
62
+ HTA11_11167 HTA11_11167_2000001011 Premalignant AD Tubular Adenoma Not Hyperplastic No Low-grade dysplasia 100% 0% 0% 0.4 Sessile 0.5 Distal Sigmoid colon Biopsy Fresh Validation Matched
63
+ HTA11_7663 HTA11_7663_2000001011 Premalignant Unknown Unknown 0.6 Biopsy Fresh Validation Matched
64
+ HTA11_7862 HTA11_7862_2000001011 Premalignant Unknown Unknown 0.7 Biopsy Fresh Validation Matched
65
+ HTA11_9341 HTA11_9341_2000001011 Premalignant Unknown Unknown 1 Biopsy Fresh Validation Matched
66
+ HTA11_10167 HTA11_10167_2000001011 Premalignant Unknown Unknown 0.5 Biopsy Fresh Validation Matched
data/cBioPortal/crc_hta11_htan_2021/data_gene_panel_matrix.txt ADDED
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1
+ SAMPLE_ID mutations
2
+ HTA11_78_2000001011 NA
3
+ HTA11_347_2000001011 WXS
4
+ HTA11_546_2000001011 NA
5
+ HTA11_104_2000001011 NA
6
+ HTA11_392_3000011011 NA
7
+ HTA11_696_2000001011 WXS
8
+ HTA11_1391_2000001011 WXS
9
+ HTA11_2951_2000001011 NA
10
+ HTA11_3361_2000001011 NA
11
+ HTA11_3410_2000001011 NA
12
+ HTA11_2235_2000001011 WXS
13
+ HTA11_5212_2000001011 WXS
14
+ HTA11_6025_2000001011 WXS
15
+ HTA11_866_2000001011 WXS
16
+ HTA11_1938_2000001011 WXS
17
+ HTA11_2487_2000001011 WXS
18
+ HTA11_3331_2000001011 WXS
19
+ HTA11_5363_2000001011 WXS
20
+ HTA11_83_2000001011 NA
21
+ HTA11_2112_2000001011 NA
22
+ HTA11_5216_2000001011 WXS
23
+ HTA11_6310_2000001011 WXS
24
+ HTA11_411_2000001011 NA
25
+ HTA11_2992_2000001011 NA
26
+ HTA11_5994_2000001011 NA
27
+ HTA11_6134_2000001011 WXS
28
+ HTA11_6147_2000001011 WXS
29
+ HTA11_866_3004761011 WXS
30
+ HTA11_3918_2000001011 WXS
31
+ HTA11_4255_2000001011 WXS
32
+ HTA11_4781_2000001011 WXS
33
+ HTA11_6182_2000001011 NA
34
+ HTA11_6298_2000001011 NA
35
+ HTA11_6801_2000001011 WXS
36
+ HTA11_6801_2000001021 NA
37
+ HTA11_6818_2000001011 NA
38
+ HTA11_6818_2000001021 NA
39
+ HTA11_7029_2000001011 NA
40
+ HTA11_7128_2000001011 NA
41
+ HTA11_7179_2000001011 NA
42
+ HTA11_7469_2000001011 NA
43
+ HTA11_7663_2000009901 WXS
44
+ HTA11_7696_3000711011 WXS
45
+ HTA11_7862_2000009901 WXS
46
+ HTA11_7956_2000001011 NA
47
+ HTA11_8099_2000001011 NA
48
+ HTA11_8622_2000001011 WXS
49
+ HTA11_8622_2000001021 WXS
50
+ HTA11_8920_2000001011 WXS
51
+ HTA11_9341_2000009901 WXS
52
+ HTA11_9408_2000001011 NA
53
+ HTA11_10167_2000009901 WXS
54
+ HTA11_10623_2000001011 WXS
55
+ HTA11_10711_2000001011 WXS
56
+ HTA11_11156_2000001011 NA
57
+ HTA11_11156_2000001021 NA
58
+ HTA11_11167_2000001011 NA
59
+ HTA11_7663_2000001011 NA
60
+ HTA11_7862_2000001011 NA
61
+ HTA11_9341_2000001011 NA
62
+ HTA11_10167_2000001011 NA
data/cBioPortal/crc_hta11_htan_2021/data_mutations.txt ADDED
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+ size 30687583
data/cBioPortal/crc_hta11_htan_2021/data_pseudo_bulk_rna_seq_expression.txt ADDED
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data/cBioPortal/crc_hta11_htan_2021/data_pseudo_bulk_rna_seq_expression_zscores_ref_all_samples.txt ADDED
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data/cBioPortal/crc_hta11_htan_2021/data_relative_fraction.txt ADDED
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1
+ ENTITY_STABLE_ID NAME ONTOLOGY_ID HTA11_78_2000001011 HTA11_83_2000001011 HTA11_104_2000001011 HTA11_347_2000001011 HTA11_392_3000011011 HTA11_411_2000001011 HTA11_546_2000001011 HTA11_696_2000001011 HTA11_866_2000001011 HTA11_866_3004761011 HTA11_1391_2000001011 HTA11_1938_2000001011 HTA11_2112_2000001011 HTA11_2235_2000001011 HTA11_2487_2000001011 HTA11_2951_2000001011 HTA11_2992_2000001011 HTA11_3331_2000001011 HTA11_3361_2000001011 HTA11_3410_2000001011 HTA11_4255_2000001011 HTA11_5212_2000001011 HTA11_5216_2000001011 HTA11_5363_2000001011 HTA11_5994_2000001011 HTA11_6025_2000001011 HTA11_6134_2000001011 HTA11_6147_2000001011 HTA11_6182_2000001011 HTA11_6298_2000001011 HTA11_6310_2000001011 HTA11_6801_2000001011 HTA11_6801_2000001021 HTA11_6818_2000001011 HTA11_6818_2000001021 HTA11_7029_2000001011 HTA11_7128_2000001011 HTA11_7179_2000001011 HTA11_7469_2000001011 HTA11_7696_3000711011 HTA11_7956_2000001011 HTA11_8099_2000001011 HTA11_8622_2000001011 HTA11_8622_2000001021 HTA11_8920_2000001011 HTA11_9408_2000001011 HTA11_10623_2000001011 HTA11_10711_2000001011 HTA11_11156_2000001011 HTA11_11156_2000001021 HTA11_11167_2000001011 HTA11_7663_2000001011 HTA11_7862_2000001011 HTA11_9341_2000001011 HTA11_10167_2000001011
2
+ ABS Absorptive Cell CL_0000212 0.186 0.578 0.517 0.672 0.054 0.374 0.476 0.411 0.468 0.04 0.051 0.084 0.397 0.255 0.37 0.264 0.638 0.376 0.465 0.116 0.346 0.9 0.675 0.826 0.545 0.681 0.272 0.29 0.053 0.182 0.416 0.369 0.506 0.108 0.064 0.041 0.173 0.393 0.824 0.085 0.691 0.356 0.129 0.165 0.493 0.236 0.539 0.259 0.245 0.41 0.468 0.576 0.438 0.591 0.646
3
+ ASC Neoplastic Cell CL_0001063 0.324 0.037 0.045 0.004 0.287 0.033 0.247 0.205 0.228 0.358 0.63 0.694 0.009 0.472 0.034 0.303 0.042 0.014 0.153 0.461 0.051 0.009 0.051 0.023 0.14 0.096 0.063 0.121 0.651 0.347 0.033 0.012 0.061 0.558 0.779 0.626 0.566 0.204 0.001 0.575 0.004 0.022 0.041 0.067 0.015 0.536 0.046 0.408 0.306 0.145 0.154 0.016 0.005 0.019 0.002
4
+ B B Cell CL_0000236 0.001 0.0 0.0 0.004 0.0 0.0 0.0 0.0 0.001 0.002 0.003 0.002 0.0 0.0 0.0 0.003 0.0 0.004 0.002 0.0 0.007 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.01 0.0 0.0 0.005 0.002 0.0 0.0 0.0 0.001 0.004 0.0 0.0 0.014 0.002 0.0 0.0 0.0 0.004 0.0 0.013 0.0 0.006 0.0 0.046 0.011
5
+ CT Intestinal Epithelial Cell CL_0002563 0.002 0.02 0.0 0.058 0.0 0.018 0.01 0.008 0.012 0.0 0.001 0.001 0.009 0.005 0.02 0.003 0.092 0.023 0.004 0.0 0.013 0.051 0.019 0.049 0.019 0.005 0.012 0.007 0.0 0.005 0.026 0.022 0.026 0.0 0.0 0.0 0.0 0.024 0.061 0.001 0.032 0.057 0.003 0.006 0.03 0.0 0.012 0.0 0.004 0.013 0.002 0.012 0.059 0.02 0.002
6
+ EE Intestinal Enteroendocrine Cell CL_1001516 0.003 0.003 0.0 0.009 0.013 0.036 0.002 0.004 0.005 0.0 0.003 0.001 0.012 0.0 0.002 0.002 0.02 0.005 0.004 0.001 0.006 0.017 0.005 0.004 0.006 0.005 0.035 0.025 0.0 0.005 0.006 0.006 0.019 0.0 0.0 0.0 0.006 0.009 0.005 0.0 0.008 0.022 0.007 0.01 0.024 0.02 0.005 0.0 0.007 0.0 0.002 0.003 0.016 0.014 0.007
7
+ END Endocytes CL_0000115 0.0 0.003 0.0 0.001 0.0 0.002 0.0 0.001 0.0 0.008 0.001 0.001 0.001 0.0 0.001 0.002 0.004 0.0 0.003 0.0 0.006 0.0 0.0 0.0 0.0 0.0 0.007 0.013 0.0 0.0 0.004 0.002 0.008 0.006 0.002 0.0 0.0 0.0 0.0 0.011 0.0 0.0 0.003 0.005 0.0 0.0 0.001 0.004 0.0 0.0 0.0 0.001 0.0 0.007 0.0
8
+ FIB Fibroblasts CL_0000057 0.0 0.002 0.0 0.002 0.0 0.001 0.0 0.0 0.0 0.002 0.0 0.004 0.0 0.0 0.0 0.0 0.0 0.0 0.003 0.001 0.0 0.0 0.0 0.0 0.0 0.0 0.007 0.007 0.0 0.0 0.014 0.002 0.002 0.005 0.002 0.0 0.012 0.0 0.0 0.009 0.0 0.0 0.003 0.001 0.0 0.0 0.02 0.002 0.0 0.025 0.003 0.008 0.019 0.002 0.004
9
+ GOB Goblet Cell CL_0000160 0.286 0.119 0.023 0.02 0.283 0.21 0.165 0.251 0.218 0.401 0.056 0.037 0.386 0.097 0.086 0.155 0.069 0.014 0.227 0.277 0.054 0.004 0.154 0.023 0.037 0.058 0.047 0.037 0.223 0.213 0.099 0.138 0.23 0.234 0.052 0.239 0.137 0.285 0.003 0.139 0.06 0.136 0.049 0.073 0.198 0.027 0.14 0.101 0.256 0.145 0.15 0.046 0.191 0.032 0.092
10
+ MAS Mast Cell CL_0000097 0.002 0.005 0.012 0.004 0.0 0.004 0.0 0.005 0.001 0.003 0.001 0.003 0.0 0.0 0.002 0.016 0.0 0.008 0.016 0.004 0.006 0.0 0.0 0.0 0.0 0.005 0.005 0.0 0.0 0.0 0.004 0.0 0.004 0.005 0.002 0.0 0.0 0.0 0.003 0.004 0.0 0.0 0.018 0.009 0.008 0.007 0.002 0.0 0.007 0.0 0.0 0.015 0.003 0.008 0.0
11
+ MYE Myleoid Cell CL_0000763 0.0 0.003 0.023 0.002 0.0 0.003 0.0 0.001 0.002 0.011 0.003 0.005 0.0 0.003 0.001 0.005 0.0 0.01 0.005 0.002 0.004 0.0 0.0 0.0 0.0 0.0 0.005 0.013 0.0 0.0 0.006 0.003 0.008 0.006 0.008 0.0 0.0 0.0 0.0 0.013 0.0 0.0 0.018 0.007 0.004 0.0 0.001 0.008 0.014 0.013 0.008 0.022 0.019 0.007 0.002
12
+ PLA Plasma Cell CL_0000786 0.019 0.049 0.045 0.032 0.0 0.004 0.001 0.004 0.006 0.007 0.005 0.019 0.001 0.0 0.002 0.121 0.0 0.041 0.041 0.015 0.025 0.0 0.0 0.0 0.0 0.015 0.03 0.0 0.003 0.0 0.014 0.003 0.003 0.019 0.033 0.0 0.012 0.0 0.009 0.009 0.0 0.0 0.082 0.011 0.012 0.0 0.011 0.006 0.007 0.037 0.0 0.15 0.01 0.028 0.017
13
+ SSC Abnormal Cell CL_0001061 0.0 0.001 0.0 0.001 0.267 0.205 0.001 0.009 0.0 0.011 0.015 0.005 0.126 0.005 0.427 0.008 0.0 0.143 0.007 0.004 0.316 0.006 0.0 0.026 0.196 0.0 0.267 0.26 0.008 0.011 0.217 0.254 0.015 0.003 0.008 0.027 0.0 0.006 0.001 0.022 0.0 0.285 0.486 0.541 0.063 0.007 0.0 0.0 0.021 0.0 0.02 0.002 0.0 0.041 0.031
14
+ STM Intestinal Crypt Stem Cell of Colon CL_0009043 0.106 0.052 0.214 0.118 0.0 0.014 0.002 0.001 0.009 0.031 0.001 0.009 0.0 0.01 0.004 0.0 0.058 0.007 0.0 0.007 0.022 0.006 0.013 0.007 0.0 0.024 0.0 0.037 0.005 0.064 0.022 0.041 0.013 0.005 0.004 0.003 0.0 0.003 0.021 0.02 0.105 0.052 0.007 0.024 0.036 0.007 0.036 0.019 0.007 0.025 0.006 0.031 0.111 0.014 0.053
15
+ T T Cell CL_0000084 0.001 0.05 0.034 0.033 0.0 0.054 0.001 0.005 0.018 0.013 0.088 0.064 0.025 0.005 0.012 0.046 0.0 0.31 0.022 0.008 0.099 0.0 0.0 0.0 0.0 0.015 0.145 0.067 0.0 0.0 0.029 0.056 0.037 0.019 0.029 0.0 0.006 0.0 0.05 0.032 0.0 0.0 0.126 0.041 0.045 0.079 0.112 0.097 0.014 0.0 0.011 0.044 0.026 0.076 0.051
16
+ TAC Transit Amplifying Cell CL_0009010 0.064 0.075 0.057 0.043 0.05 0.048 0.089 0.092 0.026 0.111 0.139 0.069 0.034 0.147 0.038 0.073 0.081 0.043 0.052 0.103 0.03 0.006 0.073 0.046 0.05 0.062 0.109 0.115 0.06 0.104 0.099 0.095 0.074 0.028 0.022 0.06 0.072 0.066 0.022 0.059 0.086 0.062 0.013 0.036 0.071 0.085 0.05 0.094 0.115 0.181 0.169 0.066 0.106 0.066 0.078
17
+ TUF Tuft Cell CL_0002204 0.01 0.011 0.034 0.004 0.05 0.002 0.01 0.01 0.013 0.012 0.009 0.008 0.005 0.005 0.009 0.008 0.0 0.01 0.004 0.008 0.023 0.006 0.015 0.0 0.011 0.039 0.0 0.019 0.003 0.074 0.008 0.005 0.0 0.005 0.001 0.006 0.018 0.012 0.005 0.023 0.016 0.012 0.006 0.011 0.008 0.0 0.03 0.002 0.004 0.0 0.011 0.01 0.005 0.038 0.011
data/cBioPortal/crc_hta11_htan_2021/data_resource_definition.txt ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ RESOURCE_ID DISPLAY_NAME RESOURCE_TYPE DESCRIPTION OPEN_BY_DEFAULT PRIORITY
2
+ HE H&E Slide SAMPLE H&E Slide TRUE 1
3
+ MXIF MxIF Image SAMPLE MxIF Images TRUE 2
data/cBioPortal/crc_hta11_htan_2021/data_resource_sample.txt ADDED
@@ -0,0 +1,98 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ PATIENT_ID SAMPLE_ID RESOURCE_ID URL
2
+ HTA11_83 HTA11_83_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25054704/elated_joliot/minerva/index.html#s=0
3
+ HTA11_83 HTA11_83_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25083429/nostalgic_saha_4/minerva/index.html#s=0
4
+ HTA11_83 HTA11_83_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25083512/nostalgic_saha_4/minerva/index.html#s=0
5
+ HTA11_83 HTA11_83_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25083552/stoic_franklin/minerva/index.html#s=0
6
+ HTA11_347 HTA11_347_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25054758/elated_joliot/minerva/index.html#s=0
7
+ HTA11_347 HTA11_347_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25078653/nostalgic_saha_4/minerva/index.html#s=0
8
+ HTA11_347 HTA11_347_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25078786/nostalgic_saha_4/minerva/index.html#s=0
9
+ HTA11_347 HTA11_347_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25078891/nostalgic_saha_4/minerva/index.html#s=0
10
+ HTA11_392 HTA11_392_3000011011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25055566/v1/minerva/index.html#s=0
11
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12
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13
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14
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15
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16
+ HTA11_392 HTA11_392_3000011011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25080243/nostalgic_saha_4/minerva/index.html#s=0
17
+ HTA11_411 HTA11_411_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25055737/v1/minerva/index.html#s=0
18
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19
+ HTA11_411 HTA11_411_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25080438/nostalgic_saha_4/minerva/index.html#s=0
20
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21
+ HTA11_546 HTA11_546_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25055779/elated_joliot/minerva/index.html#s=0
22
+ HTA11_546 HTA11_546_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25081468/stoic_franklin/minerva/index.html#s=0
23
+ HTA11_546 HTA11_546_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25081644/nostalgic_saha_4/minerva/index.html#s=0
24
+ HTA11_696 HTA11_696_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25055797/v1/minerva/index.html#s=0
25
+ HTA11_696 HTA11_696_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25083345/nostalgic_saha_4/minerva/index.html#s=0
26
+ HTA11_866 HTA11_866_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25055851/elated_joliot/minerva/index.html#s=0
27
+ HTA11_866 HTA11_866_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25083661/nostalgic_saha_4/minerva/index.html#s=0
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+ HTA11_866 HTA11_866_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25083774/nostalgic_saha_4/minerva/index.html#s=0
29
+ HTA11_1391 HTA11_1391_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25055895/elated_joliot/minerva/index.html#s=0
30
+ HTA11_1391 HTA11_1391_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25071714/stoic_franklin/minerva/index.html#s=0
31
+ HTA11_1391 HTA11_1391_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25071769/elated_poisson/minerva/index.html#s=0
32
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33
+ HTA11_1938 HTA11_1938_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25056191/v1/minerva/index.html#s=0
34
+ HTA11_1938 HTA11_1938_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25072268/nostalgic_saha_4/minerva/index.html#s=0
35
+ HTA11_1938 HTA11_1938_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25072599/nostalgic_saha_4/minerva/index.html#s=0
36
+ HTA11_2112 HTA11_2112_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25056250/elated_joliot/minerva/index.html#s=0
37
+ HTA11_2112 HTA11_2112_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25072661/nostalgic_saha_4/minerva/index.html#s=0
38
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39
+ HTA11_2112 HTA11_2112_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25072779/nostalgic_saha_4/minerva/index.html#s=0
40
+ HTA11_2112 HTA11_2112_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25072878/nostalgic_saha_4/minerva/index.html#s=0
41
+ HTA11_2235 HTA11_2235_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25056300/elated_joliot/minerva/index.html#s=0
42
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44
+ HTA11_2235 HTA11_2235_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25073076/stoic_franklin/minerva/index.html#s=0
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+ HTA11_2487 HTA11_2487_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25056480/v1/minerva/index.html#s=0
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47
+ HTA11_2487 HTA11_2487_2000001011 MXIF https://d3p249wtgzkn5u.cloudfront.net/synid/syn25073616/nostalgic_saha_4/minerva/index.html#s=0
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+ HTA11_2951 HTA11_2951_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25056808/v1/minerva/index.html#s=0
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50
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51
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+ HTA11_3331 HTA11_3331_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25058438/v1/minerva/index.html#s=0
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+ HTA11_6025 HTA11_6025_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25070310/v1/minerva/index.html#s=0
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+ HTA11_6134 HTA11_6134_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25070644/v1/minerva/index.html#s=0
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+ HTA11_6147 HTA11_6147_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25071129/v1/minerva/index.html#s=0
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+ HTA11_6310 HTA11_6310_2000001011 HE https://d3p249wtgzkn5u.cloudfront.net/synid/syn25071439/elated_joliot/minerva/index.html#s=0
95
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data/cBioPortal/crc_hta11_htan_2021/meta_absolute_counts.txt ADDED
@@ -0,0 +1,12 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ cancer_study_identifier: crc_hta11_htan_2021
2
+ genetic_alteration_type: GENERIC_ASSAY
3
+ generic_assay_type: ABSOLUTE_COUNTS
4
+ datatype: LIMIT-VALUE
5
+ stable_id: absolute_counts
6
+ profile_name: Absolute Cell Counts
7
+ profile_description: The aggregate cell count for each distinct cell type across the sample set.
8
+ data_filename: data_absolute_counts.txt
9
+ show_profile_in_analysis_tab: true
10
+ pivot_threshold_value: 0.000001
11
+ value_sort_order: ASC
12
+ generic_entity_meta_properties: NAME,ONTOLOGY_ID
data/cBioPortal/crc_hta11_htan_2021/meta_clinical_patient.txt ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ cancer_study_identifier: crc_hta11_htan_2021
2
+ data_filename: data_clinical_patient.txt
3
+ genetic_alteration_type: CLINICAL
4
+ datatype: PATIENT_ATTRIBUTES
data/cBioPortal/crc_hta11_htan_2021/meta_clinical_sample.txt ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ cancer_study_identifier: crc_hta11_htan_2021
2
+ data_filename: data_clinical_sample.txt
3
+ genetic_alteration_type: CLINICAL
4
+ datatype: SAMPLE_ATTRIBUTES
data/cBioPortal/crc_hta11_htan_2021/meta_gene_panel_matrix.txt ADDED
@@ -0,0 +1,4 @@
 
 
 
 
 
1
+ cancer_study_identifier: crc_hta11_htan_2021
2
+ genetic_alteration_type: GENE_PANEL_MATRIX
3
+ datatype: GENE_PANEL_MATRIX
4
+ data_filename: data_gene_panel_matrix.txt
data/cBioPortal/crc_hta11_htan_2021/meta_mutations.txt ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ cancer_study_identifier: crc_hta11_htan_2021
2
+ stable_id: mutations
3
+ profile_name: Mutations
4
+ profile_description: Whole exome sequencing of 30 pre-cancer colorectal polyps and their matched normals.
5
+ genetic_alteration_type: MUTATION_EXTENDED
6
+ datatype: MAF
7
+ show_profile_in_analysis_tab: true
8
+ data_filename: data_mutations.txt
data/cBioPortal/crc_hta11_htan_2021/meta_pseudo_bulk_rna_seq_expression.txt ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ cancer_study_identifier: crc_hta11_htan_2021
2
+ genetic_alteration_type: MRNA_EXPRESSION
3
+ datatype: CONTINUOUS
4
+ stable_id: rna_seq_mrna
5
+ show_profile_in_analysis_tab: FALSE
6
+ profile_name: Pseudo bulk mRNA expression
7
+ profile_description: The bulk RNA-seq counts were calculated from scRNA-seq, by averaging the expression values per sample across the cells.
8
+ data_filename: data_pseudo_bulk_rna_seq_expression.txt
data/cBioPortal/crc_hta11_htan_2021/meta_pseudo_bulk_rna_seq_expression_zscores_ref_all_samples.txt ADDED
@@ -0,0 +1,8 @@
 
 
 
 
 
 
 
 
 
1
+ cancer_study_identifier: crc_hta11_htan_2021
2
+ genetic_alteration_type: MRNA_EXPRESSION
3
+ datatype: Z-SCORE
4
+ stable_id: rna_seq_mrna_median_Zscores
5
+ show_profile_in_analysis_tab: TRUE
6
+ profile_name: Pseudo bulk mRNA expression z-scores
7
+ profile_description: The bulk RNA-seq counts were calculated from scRNA-seq, by averaging the expression values per sample across the cells (log pseudo-bulk zscores)
8
+ data_filename: data_pseudo_bulk_rna_seq_expression_zscores_ref_all_samples.txt
data/cBioPortal/crc_hta11_htan_2021/meta_relative_fraction.txt ADDED
@@ -0,0 +1,12 @@
 
 
 
 
 
 
 
 
 
 
 
 
 
1
+ cancer_study_identifier: crc_hta11_htan_2021
2
+ genetic_alteration_type: GENERIC_ASSAY
3
+ generic_assay_type: RELATIVE_COUNTS
4
+ datatype: LIMIT-VALUE
5
+ stable_id: relative_counts
6
+ profile_name: Relative Cell Counts
7
+ profile_description: The relative cell count for each distinct cell type across the sample set.
8
+ data_filename: data_relative_fraction.txt
9
+ show_profile_in_analysis_tab: true
10
+ pivot_threshold_value: 0.000001
11
+ value_sort_order: ASC
12
+ generic_entity_meta_properties: NAME,ONTOLOGY_ID
data/cBioPortal/crc_hta11_htan_2021/meta_resource_definition.txt ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ cancer_study_identifier: crc_hta11_htan_2021
2
+ resource_type: DEFINITION
3
+ data_filename: data_resource_definition.txt
data/cBioPortal/crc_hta11_htan_2021/meta_resource_sample.txt ADDED
@@ -0,0 +1,3 @@
 
 
 
 
1
+ cancer_study_identifier: crc_hta11_htan_2021
2
+ resource_type: SAMPLE
3
+ data_filename: data_resource_sample.txt
data/cBioPortal/crc_hta11_htan_2021/meta_study.txt ADDED
@@ -0,0 +1,6 @@
 
 
 
 
 
 
 
1
+ type_of_cancer: coadread
2
+ cancer_study_identifier: crc_hta11_htan_2021
3
+ name: Pre-cancer Colorectal Polyps (HTAN Vanderbilt, Cell 2021)
4
+ description: Whole-exome sequencing and single-cell transcriptomics analysis of 61 pre-malignant colorectal polyps (discovery and validation sets) and their matched normal colon tissues.
5
+ pmid: 34910928
6
+ citation: Chen et al. Cell 2021