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Browse files- initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_RNA_Seq_v2_mRNA.txt +6 -0
- initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_all.txt +6 -0
- initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_cna.txt +6 -0
- initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_cnaseq.txt +6 -0
- initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_complete.txt +6 -0
- initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_log2CNA.txt +6 -0
- initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_methylation_all.txt +6 -0
- initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_methylation_hm450.txt +6 -0
- initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_phosphoprotein_quantification.txt +6 -0
- initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_protein_quantification.txt +6 -0
- initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_rppa.txt +6 -0
- initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_sequenced.txt +6 -0
- initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_sv.txt +6 -0
- initial_data/brca_tcga_pan_can_atlas_2018/normals/meta_mrna_seq_v2_rsem_normal_samples.txt +8 -0
- initial_data/brca_tcga_pan_can_atlas_2018/normals/meta_mrna_seq_v2_rsem_normal_samples_zscores_ref_normal_samples.txt +8 -0
- initial_data/inductive_graph_residual_extension/architecture/INDUCTIVE_GR_DESIGN.md +35 -0
- initial_data/inductive_graph_residual_extension/audit/CURRENT_GR_V2_SPEC.md +43 -0
- initial_data/inductive_graph_residual_extension/audit/PHASE0_STATUS.tsv +12 -0
- initial_data/inductive_graph_residual_extension/audit/UNSEEN_NODE_CASES.tsv +4 -0
- initial_data/inductive_graph_residual_extension/audit/UNSEEN_NODE_RELATION_COVERAGE.tsv +5 -0
- initial_data/inductive_graph_residual_extension/audits/ENCODER_STATIC_SHAPE_TEST.md +14 -0
- initial_data/inductive_graph_residual_extension/audits/FEATURE_LEAKAGE_AUDIT.md +35 -0
- initial_data/inductive_graph_residual_extension/audits/INDUCTIVE_GRAPH_SPLIT_AUDIT.md +30 -0
- initial_data/inductive_graph_residual_extension/audits/PHASE1_STATUS.tsv +9 -0
- initial_data/inductive_graph_residual_extension/contracts/INDUCTIVE_FEATURE_CONTRACT.yaml +47 -0
- initial_data/inductive_graph_residual_extension/datasets/G_test_context/CONTEXT_ONLY.txt +2 -0
- initial_data/inductive_graph_residual_extension/datasets/G_test_context/graph_manifest.json +16 -0
- initial_data/inductive_graph_residual_extension/datasets/G_test_context/node_mappings/protein.tsv +0 -0
- initial_data/inductive_graph_residual_extension/datasets/G_train/graph_manifest.json +18 -0
- initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/disease.tsv +0 -0
- initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/pathway.tsv +0 -0
- initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/protein.tsv +0 -0
- initial_data/inductive_graph_residual_extension/datasets/G_train/relation_mappings.tsv +13 -0
- initial_data/inductive_graph_residual_extension/datasets/INDUCTIVE_SPLIT.tsv +0 -0
- initial_data/inductive_graph_residual_extension/feature_inventory/PROTEIN_FEATURE_INVENTORY.tsv +12 -0
- initial_data/inductive_graph_residual_extension/inductive_phase2_small/data/FEATURE_SOURCE_MANIFEST.json +24 -0
- initial_data/inductive_graph_residual_extension/inductive_phase2_small/data/PPI_SOURCE_MANIFEST.json +11 -0
- initial_data/inductive_graph_residual_extension/inductive_phase2_small/data/protein_feature_index.tsv +0 -0
- initial_data/inductive_graph_residual_extension/phase3a_link_split_audit/audits/INDUCTIVE_EDGE_CONTEXT_STATISTICS.tsv +21 -0
- initial_data/inductive_graph_residual_extension/phase3a_link_split_audit/audits/INDUCTIVE_LINK_LEAKAGE_AUDIT.tsv +7 -0
- initial_data/inductive_graph_residual_extension/phase3a_link_split_audit/logs/PHASE3A_LINK_SPLIT_AUDIT.json +30 -0
- initial_data/inductive_graph_residual_extension/phase3a_link_split_audit/reports/INDUCTIVE_LINK_SPLIT_FEASIBILITY.md +92 -0
- initial_data/inductive_graph_residual_extension/reports/CLAIM_BOUNDARY.md +27 -0
- initial_data/inductive_graph_residual_extension/reports/INDUCTIVE_EXPERIMENT_PLAN.md +46 -0
- initial_data/inductive_graph_residual_extension/reports/INDUCTIVE_GR_INTERFACE.md +56 -0
- initial_data/inductive_graph_residual_extension/reports/PHASE0_RESULT.md +29 -0
- initial_data/inductive_graph_residual_extension/reports/PHASE1_RESULT.md +34 -0
- initial_data/inductive_graph_residual_extension/split_design/INDUCTIVE_SPLIT_PROPOSAL.tsv +4 -0
- initial_data/inductive_graph_residual_extension/split_design/PROPOSED_PROTEIN_SPLIT.tsv +0 -0
- initial_data/root/final_prodisease_v32_clinvar_dataset.metadata.json +51 -0
initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_RNA_Seq_v2_mRNA.txt
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cancer_study_identifier: brca_tcga_pan_can_atlas_2018
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stable_id: brca_tcga_pan_can_atlas_2018_rna_seq_v2_mrna
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case_list_name: Samples with mRNA data (RNA Seq V2)
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case_list_description: Samples with mRNA expression data (1082 samples)
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case_list_category: all_cases_with_mrna_rnaseq_data
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case_list_ids: TCGA-OL-A66H-01 TCGA-3C-AALK-01 TCGA-AR-A1AH-01 TCGA-AC-A5EH-01 TCGA-EW-A2FW-01 TCGA-E9-A1R0-01 TCGA-B6-A2IU-01 TCGA-AR-A1AJ-01 TCGA-A7-A13G-01 TCGA-AC-A62Y-01 TCGA-E9-A1QZ-01 TCGA-E9-A1R2-01 TCGA-E9-A3X8-01 TCGA-AR-A255-01 TCGA-E2-A10B-01 TCGA-AO-A0JD-01 TCGA-EW-A2FS-01 TCGA-D8-A1XA-01 TCGA-AO-A1KQ-01 TCGA-A8-A0A6-01 TCGA-A7-A3RF-01 TCGA-A7-A3IY-01 TCGA-B6-A0IE-01 TCGA-GM-A2D9-01 TCGA-D8-A3Z5-01 TCGA-AR-A1AT-01 TCGA-AN-A03X-01 TCGA-AQ-A04J-01 TCGA-B6-A0RO-01 TCGA-E9-A1NA-01 TCGA-AC-A7VC-01 TCGA-LD-A66U-01 TCGA-AO-A0J8-01 TCGA-A8-A08R-01 TCGA-BH-A0DZ-01 TCGA-EW-A1PD-01 TCGA-E9-A1N5-01 TCGA-A8-A07B-01 TCGA-D8-A1J8-01 TCGA-B6-A0RV-01 TCGA-E2-A15R-01 TCGA-A8-A07O-01 TCGA-E9-A3QA-01 TCGA-A7-A0CE-01 TCGA-BH-A0H0-01 TCGA-A2-A3XX-01 TCGA-AC-A2FB-01 TCGA-A2-A0D4-01 TCGA-B6-A0RU-01 TCGA-A2-A0YC-01 TCGA-GM-A2DK-01 TCGA-GM-A2DC-01 TCGA-A2-A0YH-01 TCGA-AR-A24N-01 TCGA-A7-A6VV-01 TCGA-E2-A1B0-01 TCGA-BH-A1EY-01 TCGA-EW-A6S9-01 TCGA-A2-A0CQ-01 TCGA-AC-A8OS-01 TCGA-GM-A2DN-01 TCGA-AO-A03M-01 TCGA-A2-A3XT-01 TCGA-A7-A4SE-01 TCGA-BH-A0DT-01 TCGA-AC-A6IV-01 TCGA-LL-A7SZ-01 TCGA-A1-A0SJ-01 TCGA-AR-A2LJ-01 TCGA-AQ-A1H3-01 TCGA-D8-A1JB-01 TCGA-B6-A0IQ-01 TCGA-BH-A0BC-01 TCGA-BH-A1EW-01 TCGA-AO-A1KS-01 TCGA-BH-A1FG-01 TCGA-AR-A0TS-01 TCGA-AN-A0G0-01 TCGA-AO-A03T-01 TCGA-D8-A27P-01 TCGA-D8-A1JD-01 TCGA-E2-A1IL-01 TCGA-A7-A3IZ-01 TCGA-A2-A0CM-01 TCGA-AN-A04C-01 TCGA-OL-A66J-01 TCGA-AR-A2LO-01 TCGA-A8-A08L-01 TCGA-BH-A201-01 TCGA-LL-A5YM-01 TCGA-AC-A4ZE-01 TCGA-A2-A0T2-01 TCGA-A8-A06X-01 TCGA-AC-A3W5-01 TCGA-D8-A143-01 TCGA-AR-A0TP-01 TCGA-C8-A134-01 TCGA-AR-A0TZ-01 TCGA-A2-A0D2-01 TCGA-EW-A1P0-01 TCGA-A2-A4RW-01 TCGA-A2-A1G0-01 TCGA-AR-A24H-01 TCGA-D8-A1XV-01 TCGA-A8-A09B-01 TCGA-D8-A13Y-01 TCGA-AC-A2FG-01 TCGA-AR-A0TU-01 TCGA-S3-AA15-01 TCGA-C8-A12Y-01 TCGA-A8-A07L-01 TCGA-A2-A0YT-01 TCGA-A8-A07I-01 TCGA-D8-A1JI-01 TCGA-E2-A15P-01 TCGA-A8-A06T-01 TCGA-AC-A2FE-01 TCGA-B6-A0RL-01 TCGA-BH-A0HN-01 TCGA-E9-A1R6-01 TCGA-A2-A0EY-01 TCGA-D8-A1XZ-01 TCGA-E9-A1ND-01 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initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_all.txt
ADDED
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@@ -0,0 +1,6 @@
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+
cancer_study_identifier: brca_tcga_pan_can_atlas_2018
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| 2 |
+
stable_id: brca_tcga_pan_can_atlas_2018_all
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| 3 |
+
case_list_name: All samples
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| 4 |
+
case_list_description: All samples (1084 samples)
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| 5 |
+
case_list_category: all_cases_in_study
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| 6 |
+
case_list_ids: TCGA-OL-A66H-01 TCGA-3C-AALK-01 TCGA-AR-A1AH-01 TCGA-AR-A1AJ-01 TCGA-AC-A62Y-01 TCGA-E9-A1QZ-01 TCGA-E2-A10B-01 TCGA-C8-A1HL-01 TCGA-EW-A2FS-01 TCGA-D8-A1XA-01 TCGA-AO-A1KQ-01 TCGA-A8-A0A6-01 TCGA-B6-A0IE-01 TCGA-GM-A2D9-01 TCGA-AQ-A04J-01 TCGA-E9-A1RD-01 TCGA-LD-A66U-01 TCGA-BH-A1EN-01 TCGA-BH-A1FN-01 TCGA-E2-A15R-01 TCGA-E9-A3QA-01 TCGA-BH-A0H0-01 TCGA-A2-A3XX-01 TCGA-BH-A0EB-01 TCGA-E9-A3X8-01 TCGA-A7-A6VV-01 TCGA-BH-A1EY-01 TCGA-AC-A8OS-01 TCGA-BH-A18K-01 TCGA-A7-A4SE-01 TCGA-BH-A0DT-01 TCGA-AC-A6IV-01 TCGA-LL-A7SZ-01 TCGA-A1-A0SJ-01 TCGA-AR-A2LJ-01 TCGA-D8-A1X5-01 TCGA-D8-A1JB-01 TCGA-BH-A0BC-01 TCGA-AN-A0G0-01 TCGA-AO-A03T-01 TCGA-D8-A27P-01 TCGA-D8-A1JD-01 TCGA-E2-A570-01 TCGA-OL-A66J-01 TCGA-AR-A2LO-01 TCGA-E9-A5FL-01 TCGA-BH-A201-01 TCGA-LL-A5YM-01 TCGA-A2-A0T2-01 TCGA-AR-A0TP-01 TCGA-EW-A1P0-01 TCGA-A2-A4RW-01 TCGA-D8-A1XV-01 TCGA-A8-A09B-01 TCGA-D8-A13Y-01 TCGA-AR-A0TU-01 TCGA-A8-A07L-01 TCGA-A8-A07I-01 TCGA-D8-A1JI-01 TCGA-E2-A15P-01 TCGA-OL-A5RX-01 TCGA-A2-A0EY-01 TCGA-E9-A1ND-01 TCGA-XX-A89A-01 TCGA-EW-A1OY-01 TCGA-B6-A0RP-01 TCGA-LL-A9Q3-01 TCGA-A1-A0SQ-01 TCGA-AR-A5QM-01 TCGA-D8-A27V-01 TCGA-EW-A1P5-01 TCGA-BH-A18N-01 TCGA-AC-A23H-01 TCGA-BH-A0B1-01 TCGA-A2-A1FZ-01 TCGA-A7-A26H-01 TCGA-BH-A0BA-01 TCGA-E2-A2P6-01 TCGA-B6-A0RT-01 TCGA-D8-A27R-01 TCGA-LL-A442-01 TCGA-C8-A26Z-01 TCGA-AO-A1KT-01 TCGA-E2-A14Y-01 TCGA-BH-A0W4-01 TCGA-OL-A5D6-01 TCGA-AO-A0J9-01 TCGA-A8-A07E-01 TCGA-A1-A0SE-01 TCGA-E9-A3HO-01 TCGA-A8-A091-01 TCGA-D8-A1XT-01 TCGA-E9-A1NA-01 TCGA-AC-A3BB-01 TCGA-MS-A51U-01 TCGA-AC-A6IX-01 TCGA-PL-A8LY-01 TCGA-A8-A094-01 TCGA-D8-A1XJ-01 TCGA-BH-A0DG-01 TCGA-AR-A1AM-01 TCGA-4H-AAAK-01 TCGA-AC-A5EI-01 TCGA-E2-A14S-01 TCGA-A8-A06O-01 TCGA-BH-A209-01 TCGA-AR-A24S-01 TCGA-A2-A3KD-01 TCGA-D8-A1JM-01 TCGA-A8-A08P-01 TCGA-E2-A15K-01 TCGA-AC-A2FK-01 TCGA-E9-A226-01 TCGA-E2-A1AZ-01 TCGA-D8-A1X8-01 TCGA-AO-A12G-01 TCGA-C8-A1HO-01 TCGA-D8-A1XW-01 TCGA-C8-A1HM-01 TCGA-AN-A0XR-01 TCGA-AN-A0FK-01 TCGA-E9-A1RA-01 TCGA-BH-A0HA-01 TCGA-OL-A6VR-01 TCGA-LL-A740-01 TCGA-A8-A097-01 TCGA-BH-A0BZ-01 TCGA-S3-A6ZG-01 TCGA-E9-A1NG-01 TCGA-A2-A0YC-01 TCGA-AO-A0J5-01 TCGA-A2-A0EM-01 TCGA-A8-A08T-01 TCGA-AC-A6NO-01 TCGA-A2-A0CO-01 TCGA-A2-A0YI-01 TCGA-C8-A3M8-01 TCGA-BH-A0H6-01 TCGA-BH-A0BM-01 TCGA-A2-A0YD-01 TCGA-D8-A1XO-01 TCGA-AO-A12A-01 TCGA-BH-A1EX-01 TCGA-BH-A0GY-01 TCGA-C8-A26W-01 TCGA-A2-A0YM-01 TCGA-BH-A0DP-01 TCGA-GM-A2DF-01 TCGA-AR-A2LN-01 TCGA-D8-A1JF-01 TCGA-OL-A6VQ-01 TCGA-A2-A25F-01 TCGA-D8-A27G-01 TCGA-E2-A1LL-01 TCGA-C8-A273-01 TCGA-E2-A153-01 TCGA-A8-A0A1-01 TCGA-D8-A27E-01 TCGA-A7-A0CJ-01 TCGA-AR-A24W-01 TCGA-E2-A9RU-01 TCGA-AR-A0TT-01 TCGA-C8-A132-01 TCGA-E2-A10F-01 TCGA-D8-A1JJ-01 TCGA-C8-A130-01 TCGA-E2-A1B4-01 TCGA-A8-A0A4-01 TCGA-D8-A1JH-01 TCGA-S3-AA0Z-01 TCGA-BH-A0EE-01 TCGA-EW-A1IZ-01 TCGA-C8-A1HI-01 TCGA-B6-A0RQ-01 TCGA-OL-A66N-01 TCGA-A7-A4SC-01 TCGA-AR-A2LH-01 TCGA-LL-A6FR-01 TCGA-LL-A5YO-01 TCGA-E9-A1N3-01 TCGA-A8-A08Z-01 TCGA-PL-A8LV-01 TCGA-AN-A0AL-01 TCGA-E9-A24A-01 TCGA-AC-A3QQ-01 TCGA-AN-A0FW-01 TCGA-B6-A400-01 TCGA-BH-A0B9-01 TCGA-E2-A15T-01 TCGA-D8-A1X7-01 TCGA-E9-A247-01 TCGA-3C-AALI-01 TCGA-AO-A03U-01 TCGA-A8-A075-01 TCGA-AN-A041-01 TCGA-E9-A3Q9-01 TCGA-BH-A0E1-01 TCGA-BH-A0DL-01 TCGA-A1-A0SD-01 TCGA-C8-A12T-01 TCGA-E2-A158-01 TCGA-AR-A0TV-01 TCGA-AC-A2FM-01 TCGA-C8-A1HF-01 TCGA-A8-A079-01 TCGA-A2-A04Y-01 TCGA-BH-A204-01 TCGA-B6-A0WW-01 TCGA-BH-A0B4-01 TCGA-AC-A3OD-01 TCGA-E2-A154-01 TCGA-OL-A5RZ-01 TCGA-E2-A156-01 TCGA-A8-A07F-01 TCGA-AR-A24R-01 TCGA-D8-A1JL-01 TCGA-A2-A3XZ-01 TCGA-B6-A0RN-01 TCGA-A1-A0SP-01 TCGA-A2-A3Y0-01 TCGA-AC-A3YI-01 TCGA-A7-A0DB-01 TCGA-EW-A6SD-01 TCGA-A7-A426-01 TCGA-B6-A0RH-01 TCGA-A2-A4RX-01 TCGA-BH-A6R8-01 TCGA-D8-A1JP-01 TCGA-A8-A07W-01 TCGA-E9-A1N6-01 TCGA-E2-A14W-01 TCGA-AN-A0FS-01 TCGA-E9-A1NF-01 TCGA-EW-A1PA-01 TCGA-AC-A3TM-01 TCGA-D8-A27H-01 TCGA-C8-A12K-01 TCGA-AR-A2LE-01 TCGA-EW-A1PG-01 TCGA-LQ-A4E4-01 TCGA-E9-A1NC-01 TCGA-BH-A0HK-01 TCGA-GM-A4E0-01 TCGA-AO-A124-01 TCGA-S3-A6ZF-01 TCGA-D8-A1JC-01 TCGA-A8-A09D-01 TCGA-LD-A7W5-01 TCGA-A2-A3XS-01 TCGA-AR-A256-01 TCGA-A8-A06X-01 TCGA-EW-A1OW-01 TCGA-AN-A0XO-01 TCGA-BH-A0DQ-01 TCGA-B6-A2IU-01 TCGA-AR-A1AI-01 TCGA-AR-A250-01 TCGA-A2-A0T3-01 TCGA-C8-A137-01 TCGA-D8-A1JG-01 TCGA-AR-A0TZ-01 TCGA-E2-A152-01 TCGA-AN-A0XV-01 TCGA-BH-A0HN-01 TCGA-AC-A2FE-01 TCGA-C8-A1HN-01 TCGA-AR-A24V-01 TCGA-AN-A0XS-01 TCGA-A2-A4S3-01 TCGA-A2-A0CR-01 TCGA-D8-A1XY-01 TCGA-A2-A0D1-01 TCGA-E2-A1L8-01 TCGA-AN-A0FX-01 TCGA-A2-A3XU-01 TCGA-A8-A07Z-01 TCGA-AC-A62V-01 TCGA-A2-A0CK-01 TCGA-A7-A4SB-01 TCGA-AO-A0J3-01 TCGA-BH-A0AZ-01 TCGA-AO-A126-01 TCGA-AC-A8OR-01 TCGA-A2-A0YH-01 TCGA-AR-A1AO-01 TCGA-AC-A23G-01 TCGA-AN-A0FT-01 TCGA-A2-A0ST-01 TCGA-AN-A0FV-01 TCGA-C8-A275-01 TCGA-A2-A0YF-01 TCGA-AO-A129-01 TCGA-AO-A03P-01 TCGA-BH-A0DS-01 TCGA-AO-A1KO-01 TCGA-D8-A1X6-01 TCGA-EW-A3U0-01 TCGA-AQ-A7U7-01 TCGA-A2-A25A-01 TCGA-A7-A0CH-01 TCGA-AO-A12E-01 TCGA-E2-A10A-01 TCGA-C8-A1HK-01 TCGA-E9-A1R5-01 TCGA-E9-A54Y-01 TCGA-E9-A243-01 TCGA-E9-A2JS-01 TCGA-A2-A25D-01 TCGA-EW-A1J3-01 TCGA-BH-A1F8-01 TCGA-E2-A159-01 TCGA-A8-A0A7-01 TCGA-AQ-A54N-01 TCGA-A2-A04X-01 TCGA-D8-A27F-01 TCGA-A7-A0CD-01 TCGA-D8-A1JK-01 TCGA-B6-A0WV-01 TCGA-E2-A1LI-01 TCGA-A1-A0SF-01 TCGA-A8-A08X-01 TCGA-A7-A13F-01 TCGA-UL-AAZ6-01 TCGA-B6-A0RG-01 TCGA-BH-A0B5-01 TCGA-B6-A0RE-01 TCGA-BH-A208-01 TCGA-EW-A1IX-01 TCGA-BH-A1F6-01 TCGA-C8-A138-01 TCGA-BH-A0DO-01 TCGA-D8-A73U-01 TCGA-D8-A27N-01 TCGA-D8-A1X9-01 TCGA-AR-A0TR-01 TCGA-A8-A06T-01 TCGA-LL-A8F5-01 TCGA-A7-A0DC-01 TCGA-AC-A23C-01 TCGA-AR-A1AU-01 TCGA-A7-A56D-01 TCGA-AC-A3QP-01 TCGA-GM-A2DD-01 TCGA-EW-A1PH-01 TCGA-BH-A6R9-01 TCGA-C8-A8HP-01 TCGA-AR-A24X-01 TCGA-D8-A1Y0-01 TCGA-B6-A0IO-01 TCGA-A8-A07B-01 TCGA-AC-A2B8-01 TCGA-A8-A09A-01 TCGA-BH-A0H3-01 TCGA-BH-A0W7-01 TCGA-A8-A086-01 TCGA-AR-A251-01 TCGA-BH-A202-01 TCGA-BH-A0DH-01 TCGA-UU-A93S-01 TCGA-E2-A1IE-01 TCGA-AR-A1AR-01 TCGA-BH-A1FU-01 TCGA-AN-A0FN-01 TCGA-AR-A24P-01 TCGA-OL-A5RY-01 TCGA-E9-A22H-01 TCGA-D8-A3Z6-01 TCGA-E2-A155-01 TCGA-A8-A09X-01 TCGA-A8-A08J-01 TCGA-B6-A0X1-01 TCGA-B6-A0RI-01 TCGA-AN-A0AJ-01 TCGA-A2-A0SW-01 TCGA-AO-A128-01 TCGA-AR-A24T-01 TCGA-A8-A08O-01 TCGA-A8-A07U-01 TCGA-E9-A1N4-01 TCGA-A2-A0CT-01 TCGA-B6-A0RL-01 TCGA-BH-A1F2-01 TCGA-GM-A3XG-01 TCGA-E9-A1N9-01 TCGA-B6-A0I9-01 TCGA-GM-A2DM-01 TCGA-A2-A4RY-01 TCGA-S3-A6ZH-01 TCGA-C8-A12V-01 TCGA-EW-A1PF-01 TCGA-E2-A1L9-01 TCGA-E2-A14Q-01 TCGA-A7-A26E-01 TCGA-AO-A03L-01 TCGA-D8-A1J9-01 TCGA-A2-A0SY-01 TCGA-OL-A66O-01 TCGA-AC-A8OP-01 TCGA-AO-A03N-01 TCGA-E2-A1LG-01 TCGA-A7-A6VY-01 TCGA-AN-A0FY-01 TCGA-A2-A4S2-01 TCGA-AR-A1AP-01 TCGA-EW-A1PC-01 TCGA-GM-A2DA-01 TCGA-BH-A0HO-01 TCGA-EW-A6SB-01 TCGA-AC-A7VC-01 TCGA-AR-A1AN-01 TCGA-E2-A150-01 TCGA-HN-A2OB-01 TCGA-D8-A141-01 TCGA-BH-A0H5-01 TCGA-GM-A5PV-01 TCGA-OK-A5Q2-01 TCGA-A7-A6VW-01 TCGA-EW-A2FV-01 TCGA-E9-A1R3-01 TCGA-E2-A1IN-01 TCGA-AR-A254-01 TCGA-E2-A1LB-01 TCGA-BH-A18T-01 TCGA-AO-A03R-01 TCGA-E9-A54X-01 TCGA-BH-A0AV-01 TCGA-BH-A0HB-01 TCGA-A2-A0D0-01 TCGA-AO-A0JB-01 TCGA-A2-A25E-01 TCGA-AC-A3W7-01 TCGA-D8-A1JE-01 TCGA-C8-A133-01 TCGA-A2-A1G1-01 TCGA-AC-A3W5-01 TCGA-BH-A0BD-01 TCGA-A2-A3XY-01 TCGA-BH-A0HL-01 TCGA-EW-A3E8-01 TCGA-OL-A5RU-01 TCGA-A2-A0CP-01 TCGA-A7-A13G-01 TCGA-A2-A0SU-01 TCGA-E2-A1IH-01 TCGA-EW-A1IY-01 TCGA-AQ-A54O-01 TCGA-AR-A1AS-01 TCGA-D8-A1XQ-01 TCGA-A7-A0DA-01 TCGA-AC-A3HN-01 TCGA-BH-A0H7-01 TCGA-A2-A0CL-01 TCGA-AC-A6IW-01 TCGA-EW-A1J5-01 TCGA-C8-A3M7-01 TCGA-AO-A0J6-01 TCGA-C8-A274-01 TCGA-C8-A27A-01 TCGA-AR-A1AK-01 TCGA-AC-A3EH-01 TCGA-B6-A0WZ-01 TCGA-C8-A135-01 TCGA-D8-A1Y3-01 TCGA-E2-A14V-01 TCGA-D8-A1Y1-01 TCGA-EW-A2FR-01 TCGA-AO-A03V-01 TCGA-E2-A105-01 TCGA-BH-A0E2-01 TCGA-BH-A0BJ-01 TCGA-BH-A203-01 TCGA-A8-A06U-01 TCGA-E9-A1R7-01 TCGA-E2-A10E-01 TCGA-E9-A249-01 TCGA-E2-A1LK-01 TCGA-A2-A04N-01 TCGA-C8-A1HE-01 TCGA-D8-A73W-01 TCGA-A2-A0ET-01 TCGA-AO-A0JI-01 TCGA-A8-A07P-01 TCGA-E9-A245-01 TCGA-BH-A1F5-01 TCGA-AC-A23E-01 TCGA-E2-A1LA-01 TCGA-B6-A0X0-01 TCGA-A2-A0CW-01 TCGA-A2-A0CU-01 TCGA-BH-A0C7-01 TCGA-B6-A0RM-01 TCGA-BH-A0HP-01 TCGA-B6-A0I8-01 TCGA-E2-A1L7-01 TCGA-E2-A14X-01 TCGA-BH-A8FZ-01 TCGA-S3-AA17-01 TCGA-B6-A0IH-01 TCGA-C8-A12W-01 TCGA-D8-A13Z-01 TCGA-D8-A27K-01 TCGA-EW-A1J1-01 TCGA-AQ-A0Y5-01 TCGA-A8-A09W-01 TCGA-AR-A1AV-01 TCGA-A2-A0EN-01 TCGA-EW-A1PB-01 TCGA-BH-A0E9-01 TCGA-D8-A147-01 TCGA-E9-A1N8-01 TCGA-A8-A085-01 TCGA-E2-A574-01 TCGA-E2-A1IG-01 TCGA-AR-A1AX-01 TCGA-AR-A24Q-01 TCGA-BH-A1F0-01 TCGA-A8-A06Q-01 TCGA-BH-A0GZ-01 TCGA-5L-AAT0-01 TCGA-AC-A5EH-01 TCGA-EW-A2FW-01 TCGA-E9-A1R0-01 TCGA-BH-A0BL-01 TCGA-E9-A1R2-01 TCGA-GM-A2DK-01 TCGA-AR-A255-01 TCGA-AO-A0JD-01 TCGA-A8-A08L-01 TCGA-A7-A3RF-01 TCGA-A7-A3IY-01 TCGA-D8-A3Z5-01 TCGA-AR-A1AT-01 TCGA-AN-A03X-01 TCGA-B6-A0RO-01 TCGA-AR-A1AQ-01 TCGA-AO-A0J8-01 TCGA-A8-A08R-01 TCGA-BH-A0DZ-01 TCGA-EW-A1PD-01 TCGA-E9-A1N5-01 TCGA-D8-A1J8-01 TCGA-A7-A0CE-01 TCGA-A2-A0D4-01 TCGA-AN-A0XP-01 TCGA-GM-A2DC-01 TCGA-AR-A24N-01 TCGA-E2-A1B0-01 TCGA-EW-A1IW-01 TCGA-EW-A6S9-01 TCGA-A2-A0CQ-01 TCGA-GM-A2DN-01 TCGA-AO-A03M-01 TCGA-A2-A3XT-01 TCGA-AQ-A1H3-01 TCGA-B6-A1KI-01 TCGA-B6-A0IQ-01 TCGA-AO-A1KS-01 TCGA-BH-A1FG-01 TCGA-AR-A0TS-01 TCGA-AQ-A04H-01 TCGA-BH-A18R-01 TCGA-E2-A1IL-01 TCGA-A7-A3IZ-01 TCGA-A2-A0CM-01 TCGA-AN-A04C-01 TCGA-A2-A04W-01 TCGA-AC-A4ZE-01 TCGA-A8-A095-01 TCGA-D8-A143-01 TCGA-C8-A134-01 TCGA-A2-A0D2-01 TCGA-A2-A1G0-01 TCGA-AR-A24H-01 TCGA-AR-A2LQ-01 TCGA-A2-A0EP-01 TCGA-C8-A12Y-01 TCGA-A2-A0YT-01 TCGA-B6-A0X4-01 TCGA-A8-A099-01 TCGA-E9-A1R6-01 TCGA-D8-A1XZ-01 TCGA-LL-A6FQ-01 TCGA-AR-A0TY-01 TCGA-E9-A248-01 TCGA-A7-A26I-01 TCGA-E2-A1B6-01 TCGA-PE-A5DE-01 TCGA-AC-A2BM-01 TCGA-BH-A0WA-01 TCGA-BH-A42T-01 TCGA-B6-A40C-01 TCGA-BH-A0EA-01 TCGA-A2-A0CZ-01 TCGA-C8-A12Q-01 TCGA-BH-AB28-01 TCGA-A8-A09N-01 TCGA-A2-A25C-01 TCGA-OL-A5DA-01 TCGA-E2-A15A-01 TCGA-A7-A5ZV-01 TCGA-LL-A50Y-01 TCGA-B6-A0WX-01 TCGA-A2-A04Q-01 TCGA-BH-A0E0-01 TCGA-E9-A2JT-01 TCGA-AO-A0J7-01 TCGA-E2-A15G-01 TCGA-BH-A1EO-01 TCGA-C8-A12U-01 TCGA-BH-A0HQ-01 TCGA-E2-A3DX-01 TCGA-A8-A09R-01 TCGA-E2-A107-01 TCGA-A8-A076-01 TCGA-B6-A0WT-01 TCGA-D8-A1Y2-01 TCGA-BH-A0BP-01 TCGA-C8-A131-01 TCGA-D8-A1JA-01 TCGA-AN-A0AR-01 TCGA-E2-A1L6-01 TCGA-A2-A0EO-01 TCGA-BH-A0BV-01 TCGA-EW-A6SC-01 TCGA-E2-A109-01 TCGA-B6-A0I2-01 TCGA-AC-A5XS-01 TCGA-E2-A1IF-01 TCGA-AC-A2FO-01 TCGA-BH-A0C1-01 TCGA-B6-A1KF-01 TCGA-BH-A1FL-01 TCGA-A8-A06P-01 TCGA-AR-A1AY-01 TCGA-BH-A0AY-01 TCGA-AO-A0JG-01 TCGA-D8-A1XC-01 TCGA-AO-A0JE-01 TCGA-AC-A62X-01 TCGA-S3-AA11-01 TCGA-A8-A07R-01 TCGA-D8-A73X-01 TCGA-AN-A03Y-01 TCGA-A2-A0T7-01 TCGA-E9-A22G-01 TCGA-A2-A0CV-01 TCGA-D8-A27M-01 TCGA-A8-A081-01 TCGA-BH-A0RX-01 TCGA-BH-A5IZ-01 TCGA-BH-A1FH-01 TCGA-BH-A1FJ-01 TCGA-BH-A0DV-01 TCGA-AO-A03O-01 TCGA-AC-A2QJ-01 TCGA-EW-A1PE-01 TCGA-B6-A0IN-01 TCGA-A7-A2KD-01 TCGA-E2-A1II-01 TCGA-D8-A27I-01 TCGA-S3-AA14-01 TCGA-A8-A08H-01 TCGA-B6-A3ZX-01 TCGA-B6-A0IP-01 TCGA-AR-A5QP-01 TCGA-Z7-A8R5-01 TCGA-AN-A0XN-01 TCGA-A1-A0SK-01 TCGA-E9-A6HE-01 TCGA-E9-A1NI-01 TCGA-LL-A441-01 TCGA-AO-A125-01 TCGA-A8-A0A2-01 TCGA-BH-A0HI-01 TCGA-AR-A252-01 TCGA-PE-A5DC-01 TCGA-D8-A142-01 TCGA-GM-A2DO-01 TCGA-LD-A9QF-01 TCGA-AR-A0U2-01 TCGA-E2-A15L-01 TCGA-BH-A0AU-01 TCGA-A2-A0T1-01 TCGA-A8-A07C-01 TCGA-A2-A0CS-01 TCGA-EW-A1P1-01 TCGA-AC-A3W6-01 TCGA-OL-A66P-01 TCGA-B6-A1KC-01 TCGA-E9-A5UP-01 TCGA-A2-A1G4-01 TCGA-AR-A24L-01 TCGA-A2-A0D3-01 TCGA-BH-A1ET-01 TCGA-BH-A0EI-01 TCGA-AO-A0JA-01 TCGA-BH-A0DX-01 TCGA-AR-A0TX-01 TCGA-A2-A1FV-01 TCGA-LD-A74U-01 TCGA-B6-A0RU-01 TCGA-GM-A2DB-01 TCGA-E2-A15H-01 TCGA-E2-A15J-01 TCGA-E9-A244-01 TCGA-BH-A0B0-01 TCGA-A8-A093-01 TCGA-GM-A2DL-01 TCGA-EW-A1J6-01 TCGA-A8-A0AB-01 TCGA-A2-A0SV-01 TCGA-BH-A1FC-01 TCGA-E9-A22B-01 TCGA-A2-A3XV-01 TCGA-BH-A18V-01 TCGA-A2-A0EV-01 TCGA-D8-A1JT-01 TCGA-A2-A04P-01 TCGA-XX-A899-01 TCGA-BH-A18S-01 TCGA-D8-A1JN-01 TCGA-E9-A228-01 TCGA-B6-A0WY-01 TCGA-E9-A1R4-01 TCGA-A8-A08A-01 TCGA-EW-A423-01 TCGA-AN-A04A-01 TCGA-EW-A1J2-01 TCGA-A2-A04U-01 TCGA-W8-A86G-01 TCGA-A7-A5ZW-01 TCGA-E2-A56Z-01 TCGA-B6-A0IB-01 TCGA-C8-A27B-01 TCGA-A8-A096-01 TCGA-A7-A13E-01 TCGA-A2-A1G6-01 TCGA-A7-A26J-01 TCGA-E2-A14O-01 TCGA-AN-A0AS-01 TCGA-C8-A12X-01 TCGA-A7-A0D9-01 TCGA-D8-A4Z1-01 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TCGA-B6-A0IM-01 TCGA-E9-A1RF-01 TCGA-B6-A408-01 TCGA-BH-A18G-01 TCGA-LL-A73Z-01 TCGA-E2-A15E-01 TCGA-B6-A0IA-01 TCGA-A8-A090-01 TCGA-5T-A9QA-01 TCGA-A8-A08B-01 TCGA-A2-A0YG-01 TCGA-AC-A2FG-01 TCGA-E9-A1NH-01 TCGA-AR-A1AL-01 TCGA-A8-A09G-01 TCGA-BH-A28Q-01 TCGA-C8-A1HG-01 TCGA-D8-A1XK-01 TCGA-A7-A4SA-01 TCGA-3C-AAAU-01 TCGA-A2-A4S0-01 TCGA-AC-A2FB-01 TCGA-AC-A8OQ-01 TCGA-D8-A1JU-01 TCGA-C8-A12L-01 TCGA-BH-A0BT-01 TCGA-A2-A0YK-01 TCGA-A1-A0SO-01 TCGA-AR-A0U0-01 TCGA-EW-A6SA-01 TCGA-BH-A0C3-01
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initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_cna.txt
ADDED
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+
cancer_study_identifier: brca_tcga_pan_can_atlas_2018
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| 2 |
+
stable_id: brca_tcga_pan_can_atlas_2018_cna
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| 3 |
+
case_list_name: Samples with CNA data
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| 4 |
+
case_list_description: Samples with CNA data (1070 samples)
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| 5 |
+
case_list_category: all_cases_with_cna_data
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| 6 |
+
case_list_ids: TCGA-OL-A66H-01 TCGA-3C-AALK-01 TCGA-AR-A1AH-01 TCGA-AC-A5EH-01 TCGA-EW-A2FW-01 TCGA-E9-A1R0-01 TCGA-B6-A2IU-01 TCGA-AR-A1AJ-01 TCGA-A7-A13G-01 TCGA-AC-A62Y-01 TCGA-E9-A1QZ-01 TCGA-E9-A1R2-01 TCGA-E9-A3X8-01 TCGA-AR-A255-01 TCGA-E2-A10B-01 TCGA-AO-A0JD-01 TCGA-EW-A2FS-01 TCGA-D8-A1XA-01 TCGA-AO-A1KQ-01 TCGA-A8-A0A6-01 TCGA-A7-A3RF-01 TCGA-A7-A3IY-01 TCGA-B6-A0IE-01 TCGA-GM-A2D9-01 TCGA-D8-A3Z5-01 TCGA-E9-A1ND-01 TCGA-AN-A03X-01 TCGA-AQ-A04J-01 TCGA-B6-A0RO-01 TCGA-E9-A1NA-01 TCGA-AC-A7VC-01 TCGA-LD-A66U-01 TCGA-AO-A0J8-01 TCGA-A8-A08R-01 TCGA-BH-A0DZ-01 TCGA-EW-A1PD-01 TCGA-E9-A1N5-01 TCGA-A8-A07B-01 TCGA-D8-A1J8-01 TCGA-B6-A0RV-01 TCGA-E2-A15R-01 TCGA-A8-A07O-01 TCGA-E9-A3QA-01 TCGA-BH-A2L8-01 TCGA-A7-A0CE-01 TCGA-BH-A0H0-01 TCGA-A2-A3XX-01 TCGA-AC-A2FB-01 TCGA-A2-A0D4-01 TCGA-A2-A0YC-01 TCGA-GM-A2DK-01 TCGA-GM-A2DC-01 TCGA-A2-A0YH-01 TCGA-AR-A24N-01 TCGA-A7-A6VV-01 TCGA-E2-A1B0-01 TCGA-BH-A1EY-01 TCGA-EW-A6S9-01 TCGA-A2-A0CQ-01 TCGA-AC-A8OS-01 TCGA-GM-A2DN-01 TCGA-AO-A03M-01 TCGA-A2-A3XT-01 TCGA-A7-A4SE-01 TCGA-BH-A0DT-01 TCGA-AC-A6IV-01 TCGA-LL-A7SZ-01 TCGA-A1-A0SJ-01 TCGA-AR-A2LJ-01 TCGA-AQ-A1H3-01 TCGA-D8-A1JB-01 TCGA-B6-A0IQ-01 TCGA-BH-A0BC-01 TCGA-BH-A1EW-01 TCGA-AO-A1KS-01 TCGA-BH-A1FG-01 TCGA-AR-A0TS-01 TCGA-C8-A1HL-01 TCGA-AO-A03T-01 TCGA-D8-A27P-01 TCGA-D8-A1JD-01 TCGA-E2-A1IL-01 TCGA-A7-A3IZ-01 TCGA-A2-A0CM-01 TCGA-AN-A04C-01 TCGA-OL-A66J-01 TCGA-AR-A2LO-01 TCGA-A8-A08L-01 TCGA-BH-A201-01 TCGA-LL-A5YM-01 TCGA-AC-A4ZE-01 TCGA-A2-A0T2-01 TCGA-A8-A06X-01 TCGA-AC-A3W5-01 TCGA-D8-A143-01 TCGA-AR-A0TP-01 TCGA-C8-A134-01 TCGA-AR-A0TZ-01 TCGA-A2-A0D2-01 TCGA-EW-A1P0-01 TCGA-A2-A4RW-01 TCGA-A2-A1G0-01 TCGA-AR-A24H-01 TCGA-D8-A1XV-01 TCGA-A8-A09B-01 TCGA-D8-A13Y-01 TCGA-AC-A2FG-01 TCGA-S3-AA15-01 TCGA-C8-A12Y-01 TCGA-A8-A07L-01 TCGA-A2-A0YT-01 TCGA-A8-A07I-01 TCGA-D8-A1JI-01 TCGA-E2-A15P-01 TCGA-A8-A06T-01 TCGA-UU-A93S-01 TCGA-B6-A0RL-01 TCGA-E9-A1R6-01 TCGA-A2-A0EY-01 TCGA-D8-A1XZ-01 TCGA-AC-A2FE-01 TCGA-BH-A0H3-01 TCGA-XX-A89A-01 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TCGA-E9-A54X-01 TCGA-AN-A0AM-01 TCGA-LD-A9QF-01 TCGA-BH-A0AV-01 TCGA-BH-A0HB-01 TCGA-A2-A0D0-01 TCGA-AO-A0JB-01 TCGA-BH-A0W5-01 TCGA-A2-A25E-01 TCGA-AO-A12H-01 TCGA-AC-A3W7-01 TCGA-AR-A0U2-01 TCGA-C8-A133-01 TCGA-A2-A1G1-01 TCGA-E2-A10E-01 TCGA-A7-A13D-01 TCGA-A2-A3XY-01 TCGA-E2-A15S-01 TCGA-A8-A09W-01 TCGA-AR-A24K-01 TCGA-E9-A1RI-01 TCGA-GM-A2DI-01 TCGA-A2-A0T6-01 TCGA-EW-A1OZ-01 TCGA-BH-A0B7-01 TCGA-EW-A3E8-01 TCGA-OL-A5RU-01 TCGA-S3-AA12-01 TCGA-B6-A0RM-01 TCGA-A2-A1FX-01 TCGA-D8-A73U-01 TCGA-A2-A0CP-01 TCGA-BH-A0BG-01 TCGA-E2-A10F-01 TCGA-A7-A4SD-01 TCGA-A2-A0YG-01 TCGA-A7-A3J0-01 TCGA-GM-A3NY-01 TCGA-AQ-A1H2-01 TCGA-D8-A27T-01 TCGA-E2-A1IH-01 TCGA-EW-A1IY-01 TCGA-B6-A0X4-01 TCGA-AR-A1AS-01 TCGA-BH-A0HY-01 TCGA-E2-A15I-01 TCGA-D8-A1XQ-01 TCGA-A7-A0DA-01 TCGA-C8-A278-01 TCGA-AC-A3HN-01 TCGA-BH-A28O-01 TCGA-AR-A24Q-01 TCGA-A2-A0EU-01 TCGA-BH-A1FE-01 TCGA-BH-A0H7-01 TCGA-A2-A0EN-01 TCGA-A8-A09C-01 TCGA-A2-A0CL-01 TCGA-BH-A18L-01 TCGA-A1-A0SG-01 TCGA-AC-A6IW-01 TCGA-A2-A0EX-01 TCGA-EW-A1J5-01 TCGA-WT-AB41-01 TCGA-LL-A5YL-01 TCGA-A2-A04T-01 TCGA-AO-A0J6-01 TCGA-C8-A1HJ-01 TCGA-C8-A274-01 TCGA-C8-A27A-01 TCGA-AR-A1AK-01 TCGA-AC-A3EH-01 TCGA-AR-A0TQ-01 TCGA-B6-A0WZ-01 TCGA-GM-A4E0-01 TCGA-A8-A0AD-01 TCGA-C8-A26X-01 TCGA-BH-A5IZ-01 TCGA-E9-A22A-01 TCGA-A7-A3J1-01 TCGA-BH-A0BO-01 TCGA-A2-A04P-01 TCGA-D8-A1Y3-01 TCGA-AC-A3YJ-01 TCGA-E9-A22E-01 TCGA-A2-A0EQ-01 TCGA-D8-A1XW-01 TCGA-D8-A1Y1-01 TCGA-BH-A0DK-01 TCGA-AN-A0FL-01 TCGA-C8-A12O-01 TCGA-C8-A12M-01 TCGA-EW-A2FR-01 TCGA-BH-A18P-01 TCGA-S3-A6ZF-01 TCGA-E2-A105-01 TCGA-PL-A8LZ-01 TCGA-A7-A13F-01 TCGA-BH-A0E2-01 TCGA-BH-A0BJ-01 TCGA-BH-A203-01 TCGA-AR-A0U4-01 TCGA-E2-A1B5-01 TCGA-A8-A06U-01 TCGA-LL-A73Y-01 TCGA-E9-A1R7-01 TCGA-E2-A14U-01 TCGA-OL-A66P-01 TCGA-E9-A249-01 TCGA-LL-A442-01 TCGA-AC-A2BK-01 TCGA-BH-A0BD-01 TCGA-E2-A1BD-01 TCGA-BH-A0DE-01 TCGA-E2-A1LK-01 TCGA-E2-A15O-01 TCGA-LD-A7W6-01 TCGA-A2-A04N-01 TCGA-C8-A1HE-01 TCGA-D8-A1XM-01 TCGA-AC-A7VB-01 TCGA-D8-A1JH-01 TCGA-D8-A1XS-01 TCGA-E9-A227-01 TCGA-A2-A0ET-01 TCGA-AO-A0JI-01 TCGA-BH-A1EU-01 TCGA-AN-A0FT-01 TCGA-OL-A97C-01 TCGA-PE-A5DD-01 TCGA-E9-A245-01 TCGA-OL-A6VO-01 TCGA-5L-AAT0-01 TCGA-A7-A0CG-01 TCGA-AC-A23E-01 TCGA-BH-A0B3-01 TCGA-E2-A1LA-01 TCGA-B6-A40B-01 TCGA-B6-A0X0-01 TCGA-D8-A145-01 TCGA-WT-AB44-01 TCGA-EW-A424-01 TCGA-BH-A1FR-01 TCGA-A2-A0CW-01 TCGA-A7-A425-01 TCGA-B6-A0IK-01 TCGA-A2-A0CU-01 TCGA-C8-A8HR-01 TCGA-E9-A1RF-01 TCGA-B6-A408-01 TCGA-AN-A0FD-01 TCGA-BH-A18G-01 TCGA-LL-A73Z-01 TCGA-E2-A15E-01 TCGA-E2-A1L7-01 TCGA-A8-A07P-01 TCGA-A2-A0YE-01 TCGA-A8-A08B-01 TCGA-D8-A1XR-01 TCGA-BH-A8FZ-01 TCGA-S3-AA17-01 TCGA-B6-A0IH-01 TCGA-AO-A0J2-01 TCGA-AR-A1AL-01 TCGA-EW-A1IZ-01 TCGA-C8-A12W-01 TCGA-BH-A1EO-01 TCGA-A8-A09G-01 TCGA-D8-A13Z-01 TCGA-D8-A27K-01 TCGA-BH-A28Q-01 TCGA-EW-A1J1-01 TCGA-AO-A03O-01 TCGA-C8-A1HG-01 TCGA-D8-A1XK-01 TCGA-AQ-A0Y5-01 TCGA-3C-AAAU-01 TCGA-A2-A4S0-01 TCGA-B6-A0IM-01 TCGA-AC-A8OQ-01 TCGA-E2-A3DX-01 TCGA-EW-A1PB-01 TCGA-D8-A1JU-01 TCGA-C8-A12L-01 TCGA-E2-A108-01 TCGA-BH-A0BT-01 TCGA-A2-A0YK-01 TCGA-E9-A1N8-01 TCGA-A8-A085-01 TCGA-AN-A0FZ-01 TCGA-B6-A402-01 TCGA-A1-A0SO-01 TCGA-BH-A0DI-01 TCGA-E2-A1IG-01 TCGA-EW-A6SC-01 TCGA-B6-A0IA-01 TCGA-E9-A1NH-01 TCGA-EW-A6SA-01 TCGA-BH-A0C3-01 TCGA-BH-A1F0-01 TCGA-A8-A06Q-01 TCGA-BH-A0GZ-01 TCGA-AR-A0U0-01
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initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_cnaseq.txt
ADDED
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+
cancer_study_identifier: brca_tcga_pan_can_atlas_2018
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| 2 |
+
stable_id: brca_tcga_pan_can_atlas_2018_cnaseq
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| 3 |
+
case_list_name: Samples with mutation and CNA data
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| 4 |
+
case_list_description: Samples with mutation and CNA data (996 samples)
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| 5 |
+
case_list_category: all_cases_with_mutation_and_cna_data
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| 6 |
+
case_list_ids: TCGA-OL-A66H-01 TCGA-3C-AALK-01 TCGA-AR-A1AH-01 TCGA-AC-A5EH-01 TCGA-EW-A2FW-01 TCGA-E9-A1R0-01 TCGA-B6-A2IU-01 TCGA-AR-A1AJ-01 TCGA-A7-A13G-01 TCGA-AC-A62Y-01 TCGA-E9-A1QZ-01 TCGA-E9-A1R2-01 TCGA-E9-A3X8-01 TCGA-AR-A255-01 TCGA-E2-A10B-01 TCGA-AO-A0JD-01 TCGA-EW-A2FS-01 TCGA-D8-A1XA-01 TCGA-A8-A08L-01 TCGA-A8-A0A6-01 TCGA-AN-A0XL-01 TCGA-B6-A0IE-01 TCGA-GM-A2D9-01 TCGA-E9-A1ND-01 TCGA-AN-A03X-01 TCGA-AQ-A04J-01 TCGA-B6-A0RO-01 TCGA-E9-A1NA-01 TCGA-AC-A7VC-01 TCGA-LD-A66U-01 TCGA-AO-A0J8-01 TCGA-A8-A08R-01 TCGA-BH-A0DZ-01 TCGA-EW-A1PD-01 TCGA-E9-A1N5-01 TCGA-A8-A07B-01 TCGA-D8-A1J8-01 TCGA-E2-A15R-01 TCGA-A8-A07O-01 TCGA-E9-A3QA-01 TCGA-BH-A2L8-01 TCGA-A7-A0CE-01 TCGA-LL-A6FR-01 TCGA-A2-A3XX-01 TCGA-AC-A2FB-01 TCGA-A2-A0D4-01 TCGA-A2-A0YC-01 TCGA-GM-A2DK-01 TCGA-GM-A2DC-01 TCGA-A2-A0YH-01 TCGA-AR-A24N-01 TCGA-D8-A27T-01 TCGA-A7-A6VV-01 TCGA-E2-A1B0-01 TCGA-BH-A1EY-01 TCGA-EW-A6S9-01 TCGA-A2-A0CQ-01 TCGA-AQ-A0Y5-01 TCGA-AC-A8OS-01 TCGA-GM-A2DN-01 TCGA-AO-A03M-01 TCGA-A2-A3XT-01 TCGA-A7-A4SE-01 TCGA-BH-A0DT-01 TCGA-AC-A6IV-01 TCGA-LL-A7SZ-01 TCGA-A1-A0SJ-01 TCGA-C8-A1HM-01 TCGA-AQ-A1H3-01 TCGA-D8-A1JB-01 TCGA-B6-A0IQ-01 TCGA-BH-A0BC-01 TCGA-BH-A1EW-01 TCGA-AO-A1KS-01 TCGA-BH-A1FG-01 TCGA-AR-A0TS-01 TCGA-C8-A1HL-01 TCGA-AO-A03T-01 TCGA-D8-A27P-01 TCGA-D8-A1JD-01 TCGA-E2-A1IL-01 TCGA-AR-A24O-01 TCGA-A2-A0CM-01 TCGA-AN-A04C-01 TCGA-OL-A66J-01 TCGA-AR-A2LO-01 TCGA-A2-A04W-01 TCGA-BH-A201-01 TCGA-LL-A5YM-01 TCGA-AC-A4ZE-01 TCGA-A2-A0T2-01 TCGA-A8-A06X-01 TCGA-D8-A143-01 TCGA-AR-A0TP-01 TCGA-C8-A134-01 TCGA-AR-A0TZ-01 TCGA-A2-A0D2-01 TCGA-EW-A1P0-01 TCGA-A2-A1G0-01 TCGA-AR-A24H-01 TCGA-BH-A1FU-01 TCGA-A7-A3RF-01 TCGA-D8-A13Y-01 TCGA-AN-A0XV-01 TCGA-C8-A12Y-01 TCGA-A8-A07L-01 TCGA-A2-A0YT-01 TCGA-A8-A07I-01 TCGA-D8-A1JI-01 TCGA-E2-A15P-01 TCGA-A8-A06T-01 TCGA-UU-A93S-01 TCGA-B6-A0RL-01 TCGA-E9-A1R6-01 TCGA-A2-A0EY-01 TCGA-D8-A1XZ-01 TCGA-BH-A0H3-01 TCGA-XX-A89A-01 TCGA-EW-A1OY-01 TCGA-A8-A08X-01 TCGA-AR-A0TY-01 TCGA-A2-A0SY-01 TCGA-LL-A9Q3-01 TCGA-A1-A0SQ-01 TCGA-AR-A5QM-01 TCGA-A2-A0SW-01 TCGA-EW-A1P5-01 TCGA-PE-A5DE-01 TCGA-BH-A18N-01 TCGA-A2-A0ST-01 TCGA-E9-A1RD-01 TCGA-AC-A23H-01 TCGA-AC-A2BM-01 TCGA-BH-A0WA-01 TCGA-AC-A3QQ-01 TCGA-AN-A0FW-01 TCGA-B6-A40C-01 TCGA-BH-A0EA-01 TCGA-A2-A1FZ-01 TCGA-C8-A12Q-01 TCGA-A2-A0SV-01 TCGA-BH-A0BA-01 TCGA-BH-AB28-01 TCGA-A8-A09N-01 TCGA-E2-A2P6-01 TCGA-B6-A0RT-01 TCGA-AR-A1AY-01 TCGA-A2-A25C-01 TCGA-S3-AA10-01 TCGA-OL-A5DA-01 TCGA-D8-A27R-01 TCGA-E2-A15A-01 TCGA-A7-A5ZV-01 TCGA-LL-A50Y-01 TCGA-B6-A0WX-01 TCGA-BH-A1EN-01 TCGA-C8-A26Z-01 TCGA-A2-A04Q-01 TCGA-E2-A14Y-01 TCGA-BH-A1FN-01 TCGA-BH-A0E0-01 TCGA-E9-A2JT-01 TCGA-OL-A5D6-01 TCGA-AR-A0U1-01 TCGA-A2-A4S3-01 TCGA-E2-A15G-01 TCGA-AO-A0J9-01 TCGA-C8-A12U-01 TCGA-A8-A09X-01 TCGA-BH-A0HQ-01 TCGA-A8-A07E-01 TCGA-A1-A0SE-01 TCGA-A8-A09R-01 TCGA-E2-A107-01 TCGA-E9-A3HO-01 TCGA-A8-A091-01 TCGA-A8-A076-01 TCGA-D8-A1XT-01 TCGA-AR-A1AQ-01 TCGA-AR-A24U-01 TCGA-BH-A42V-01 TCGA-AC-A6IX-01 TCGA-B6-A0WT-01 TCGA-D8-A1Y2-01 TCGA-PL-A8LY-01 TCGA-A2-A0EV-01 TCGA-BH-A0BP-01 TCGA-C8-A131-01 TCGA-D8-A1XJ-01 TCGA-BH-A0DG-01 TCGA-WT-AB41-01 TCGA-BH-A18M-01 TCGA-D8-A1JA-01 TCGA-AN-A0AR-01 TCGA-E2-A1L6-01 TCGA-A2-A0EO-01 TCGA-BH-A0BV-01 TCGA-D8-A27G-01 TCGA-AN-A0FN-01 TCGA-E2-A109-01 TCGA-B6-A0I2-01 TCGA-AO-A0J3-01 TCGA-4H-AAAK-01 TCGA-AC-A5XS-01 TCGA-AC-A5EI-01 TCGA-3C-AALI-01 TCGA-E2-A1IF-01 TCGA-A8-A06O-01 TCGA-AC-A2FO-01 TCGA-BH-A209-01 TCGA-AR-A24S-01 TCGA-A2-A3KD-01 TCGA-D8-A1JM-01 TCGA-BH-A1FL-01 TCGA-A8-A06P-01 TCGA-E2-A15K-01 TCGA-E9-A1NI-01 TCGA-BH-A0AY-01 TCGA-AC-A2FK-01 TCGA-E9-A226-01 TCGA-AR-A2LE-01 TCGA-E2-A1AZ-01 TCGA-D8-A1X8-01 TCGA-B6-A0WY-01 TCGA-A2-A0T5-01 TCGA-BH-A0EI-01 TCGA-C8-A1HO-01 TCGA-LD-A74U-01 TCGA-AO-A0JE-01 TCGA-AC-A62X-01 TCGA-AN-A0XR-01 TCGA-AN-A0FK-01 TCGA-AN-A0AT-01 TCGA-E9-A1RA-01 TCGA-AN-A03Y-01 TCGA-A2-A0T7-01 TCGA-BH-A0EB-01 TCGA-OL-A6VR-01 TCGA-E9-A22G-01 TCGA-LL-A740-01 TCGA-A2-A0CV-01 TCGA-BH-A0C1-01 TCGA-AC-A2QH-01 TCGA-D8-A27M-01 TCGA-A8-A081-01 TCGA-BH-A0BZ-01 TCGA-BH-A0RX-01 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TCGA-BH-A0C3-01 TCGA-BH-A1F0-01 TCGA-A8-A06Q-01 TCGA-BH-A0GZ-01 TCGA-AR-A0U0-01
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initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_complete.txt
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cancer_study_identifier: brca_tcga_pan_can_atlas_2018
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| 2 |
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stable_id: brca_tcga_pan_can_atlas_2018_3way_complete
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| 3 |
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case_list_name: Complete samples
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| 4 |
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case_list_description: Samples with mutation, CNA and expression data (994 samples)
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| 5 |
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case_list_category: all_cases_with_mutation_and_cna_and_mrna_data
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| 6 |
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case_list_ids: TCGA-OL-A66H-01 TCGA-3C-AALK-01 TCGA-AR-A1AH-01 TCGA-AC-A5EH-01 TCGA-EW-A2FW-01 TCGA-E9-A1R0-01 TCGA-B6-A2IU-01 TCGA-AR-A1AJ-01 TCGA-A7-A13G-01 TCGA-AC-A62Y-01 TCGA-E9-A1QZ-01 TCGA-E9-A1R2-01 TCGA-E9-A3X8-01 TCGA-AR-A255-01 TCGA-E2-A10B-01 TCGA-AO-A0JD-01 TCGA-EW-A2FS-01 TCGA-D8-A1XA-01 TCGA-A8-A08L-01 TCGA-A8-A0A6-01 TCGA-AN-A0XL-01 TCGA-B6-A0IE-01 TCGA-GM-A2D9-01 TCGA-E9-A1ND-01 TCGA-AN-A03X-01 TCGA-AQ-A04J-01 TCGA-B6-A0RO-01 TCGA-E9-A1NA-01 TCGA-AC-A7VC-01 TCGA-LD-A66U-01 TCGA-AO-A0J8-01 TCGA-A8-A08R-01 TCGA-BH-A0DZ-01 TCGA-EW-A1PD-01 TCGA-E9-A1N5-01 TCGA-A8-A07B-01 TCGA-D8-A1J8-01 TCGA-E2-A15R-01 TCGA-A8-A07O-01 TCGA-E9-A3QA-01 TCGA-BH-A2L8-01 TCGA-A7-A0CE-01 TCGA-LL-A6FR-01 TCGA-A2-A3XX-01 TCGA-AC-A2FB-01 TCGA-A2-A0D4-01 TCGA-A2-A0YC-01 TCGA-GM-A2DK-01 TCGA-GM-A2DC-01 TCGA-A2-A0YH-01 TCGA-AR-A24N-01 TCGA-D8-A27T-01 TCGA-A7-A6VV-01 TCGA-E2-A1B0-01 TCGA-BH-A1EY-01 TCGA-EW-A6S9-01 TCGA-A2-A0CQ-01 TCGA-AQ-A0Y5-01 TCGA-E9-A1N3-01 TCGA-GM-A2DN-01 TCGA-AO-A03M-01 TCGA-A2-A3XT-01 TCGA-A7-A4SE-01 TCGA-BH-A0DT-01 TCGA-AC-A6IV-01 TCGA-LL-A7SZ-01 TCGA-A1-A0SJ-01 TCGA-C8-A1HM-01 TCGA-AQ-A1H3-01 TCGA-D8-A1JB-01 TCGA-B6-A0IQ-01 TCGA-BH-A0BC-01 TCGA-BH-A1EW-01 TCGA-AO-A1KS-01 TCGA-BH-A1FG-01 TCGA-AR-A0TS-01 TCGA-C8-A1HL-01 TCGA-AO-A03T-01 TCGA-D8-A27P-01 TCGA-D8-A1JD-01 TCGA-E2-A1IL-01 TCGA-AR-A24O-01 TCGA-A2-A0CM-01 TCGA-AN-A04C-01 TCGA-OL-A66J-01 TCGA-AR-A2LO-01 TCGA-A2-A04W-01 TCGA-BH-A201-01 TCGA-LL-A5YM-01 TCGA-AC-A4ZE-01 TCGA-A2-A0T2-01 TCGA-A8-A06X-01 TCGA-D8-A143-01 TCGA-AR-A0TP-01 TCGA-C8-A134-01 TCGA-AR-A0TZ-01 TCGA-A2-A0D2-01 TCGA-EW-A1P0-01 TCGA-A2-A1G0-01 TCGA-AR-A24H-01 TCGA-BH-A1FU-01 TCGA-A7-A3RF-01 TCGA-D8-A13Y-01 TCGA-AN-A0XV-01 TCGA-C8-A12Y-01 TCGA-A8-A07L-01 TCGA-A2-A0YT-01 TCGA-A8-A07I-01 TCGA-D8-A1JI-01 TCGA-E2-A15P-01 TCGA-A8-A06T-01 TCGA-UU-A93S-01 TCGA-B6-A0RL-01 TCGA-E9-A1R6-01 TCGA-A2-A0EY-01 TCGA-D8-A1XZ-01 TCGA-BH-A0H3-01 TCGA-XX-A89A-01 TCGA-EW-A1OY-01 TCGA-A8-A08X-01 TCGA-AR-A0TY-01 TCGA-A2-A0SY-01 TCGA-LL-A9Q3-01 TCGA-A1-A0SQ-01 TCGA-AR-A5QM-01 TCGA-A2-A0SW-01 TCGA-EW-A1P5-01 TCGA-PE-A5DE-01 TCGA-BH-A18N-01 TCGA-A2-A0ST-01 TCGA-E9-A1RD-01 TCGA-AC-A23H-01 TCGA-AC-A2BM-01 TCGA-BH-A0WA-01 TCGA-AC-A3QQ-01 TCGA-AN-A0FW-01 TCGA-B6-A40C-01 TCGA-BH-A0EA-01 TCGA-A2-A1FZ-01 TCGA-C8-A12Q-01 TCGA-A2-A0SV-01 TCGA-BH-A0BA-01 TCGA-BH-AB28-01 TCGA-A8-A09N-01 TCGA-E2-A2P6-01 TCGA-B6-A0RT-01 TCGA-AR-A1AY-01 TCGA-A2-A25C-01 TCGA-S3-AA10-01 TCGA-OL-A5DA-01 TCGA-D8-A27R-01 TCGA-E2-A15A-01 TCGA-A7-A5ZV-01 TCGA-LL-A50Y-01 TCGA-B6-A0WX-01 TCGA-BH-A1EN-01 TCGA-C8-A26Z-01 TCGA-A2-A04Q-01 TCGA-E2-A14Y-01 TCGA-BH-A1FN-01 TCGA-BH-A0E0-01 TCGA-E9-A2JT-01 TCGA-OL-A5D6-01 TCGA-AR-A0U1-01 TCGA-A2-A4S3-01 TCGA-E2-A15G-01 TCGA-AO-A0J9-01 TCGA-C8-A12U-01 TCGA-A8-A09X-01 TCGA-BH-A0HQ-01 TCGA-A8-A07E-01 TCGA-A1-A0SE-01 TCGA-A8-A09R-01 TCGA-E2-A107-01 TCGA-E9-A3HO-01 TCGA-A8-A091-01 TCGA-A8-A076-01 TCGA-D8-A1XT-01 TCGA-AR-A1AQ-01 TCGA-AR-A24U-01 TCGA-BH-A42V-01 TCGA-AC-A6IX-01 TCGA-B6-A0WT-01 TCGA-D8-A1Y2-01 TCGA-PL-A8LY-01 TCGA-A2-A0EV-01 TCGA-BH-A0BP-01 TCGA-C8-A131-01 TCGA-D8-A1XJ-01 TCGA-BH-A0DG-01 TCGA-WT-AB41-01 TCGA-BH-A18M-01 TCGA-D8-A1JA-01 TCGA-AN-A0AR-01 TCGA-E2-A1L6-01 TCGA-A2-A0EO-01 TCGA-BH-A0BV-01 TCGA-D8-A27G-01 TCGA-AN-A0FN-01 TCGA-E2-A109-01 TCGA-B6-A0I2-01 TCGA-AO-A0J3-01 TCGA-4H-AAAK-01 TCGA-AC-A5XS-01 TCGA-3C-AALI-01 TCGA-E2-A1IF-01 TCGA-A8-A06O-01 TCGA-AC-A2FO-01 TCGA-BH-A209-01 TCGA-AR-A24S-01 TCGA-A2-A3KD-01 TCGA-D8-A1JM-01 TCGA-BH-A1FL-01 TCGA-A8-A06P-01 TCGA-E2-A15K-01 TCGA-E9-A1NI-01 TCGA-BH-A0AY-01 TCGA-AC-A2FK-01 TCGA-E9-A226-01 TCGA-AR-A2LE-01 TCGA-E2-A1AZ-01 TCGA-D8-A1X8-01 TCGA-B6-A0WY-01 TCGA-A2-A0T5-01 TCGA-BH-A0EI-01 TCGA-C8-A1HO-01 TCGA-LD-A74U-01 TCGA-AO-A0JE-01 TCGA-AC-A62X-01 TCGA-AN-A0XR-01 TCGA-AN-A0FK-01 TCGA-AN-A0AT-01 TCGA-E9-A1RA-01 TCGA-AN-A03Y-01 TCGA-A2-A0T7-01 TCGA-BH-A0EB-01 TCGA-OL-A6VR-01 TCGA-E9-A22G-01 TCGA-LL-A740-01 TCGA-A2-A0CV-01 TCGA-BH-A0C1-01 TCGA-AC-A2QH-01 TCGA-D8-A27M-01 TCGA-A8-A081-01 TCGA-BH-A0BZ-01 TCGA-BH-A0RX-01 TCGA-S3-A6ZG-01 TCGA-E9-A1NG-01 TCGA-AN-A0XP-01 TCGA-C8-A135-01 TCGA-AO-A0J5-01 TCGA-BH-A1F5-01 TCGA-A2-A0EM-01 TCGA-A8-A08T-01 TCGA-B6-A1KF-01 TCGA-BH-A1FJ-01 TCGA-BH-A0DV-01 TCGA-A8-A07Z-01 TCGA-A8-A08P-01 TCGA-A2-A0YI-01 TCGA-AN-A0FZ-01 TCGA-EW-A1PE-01 TCGA-B6-A0IN-01 TCGA-BH-A0H6-01 TCGA-BH-A0BM-01 TCGA-A7-A2KD-01 TCGA-E2-A1II-01 TCGA-D8-A27I-01 TCGA-S3-AA14-01 TCGA-A8-A08H-01 TCGA-D8-A1XO-01 TCGA-B6-A0IP-01 TCGA-EW-A1IW-01 TCGA-AR-A5QP-01 TCGA-E2-A14V-01 TCGA-AN-A0XN-01 TCGA-AC-A62V-01 TCGA-BH-A0E9-01 TCGA-A1-A0SK-01 TCGA-E9-A6HE-01 TCGA-AO-A12A-01 TCGA-BH-A1EX-01 TCGA-AO-A125-01 TCGA-C8-A26W-01 TCGA-A8-A0A2-01 TCGA-A2-A0YM-01 TCGA-BH-A0DP-01 TCGA-A2-A0CK-01 TCGA-AR-A2LN-01 TCGA-D8-A1JF-01 TCGA-OL-A6VQ-01 TCGA-BH-A0HI-01 TCGA-AR-A252-01 TCGA-A2-A25F-01 TCGA-PE-A5DC-01 TCGA-D8-A142-01 TCGA-GM-A2DO-01 TCGA-E2-A1LL-01 TCGA-C8-A273-01 TCGA-B6-A0RI-01 TCGA-E2-A153-01 TCGA-A8-A0A1-01 TCGA-E2-A15L-01 TCGA-BH-A0AU-01 TCGA-A2-A0T1-01 TCGA-A7-A0CJ-01 TCGA-BH-A18P-01 TCGA-A2-A0CS-01 TCGA-AR-A24W-01 TCGA-EW-A1P1-01 TCGA-E2-A9RU-01 TCGA-AR-A0TT-01 TCGA-C8-A132-01 TCGA-BH-A0W4-01 TCGA-E2-A10F-01 TCGA-D8-A1JJ-01 TCGA-C8-A130-01 TCGA-E2-A1B4-01 TCGA-A8-A0A4-01 TCGA-B6-A1KC-01 TCGA-A2-A1G4-01 TCGA-AR-A24L-01 TCGA-A2-A0D3-01 TCGA-BH-A1ET-01 TCGA-AO-A12G-01 TCGA-AO-A0JA-01 TCGA-BH-A0EE-01 TCGA-BH-A0DX-01 TCGA-AR-A0TX-01 TCGA-AO-A0JG-01 TCGA-OL-A66N-01 TCGA-A2-A1FV-01 TCGA-D8-A1XC-01 TCGA-AR-A2LH-01 TCGA-BH-A0H0-01 TCGA-B6-A0RU-01 TCGA-GM-A2DB-01 TCGA-LL-A5YO-01 TCGA-AC-A8OS-01 TCGA-A8-A08Z-01 TCGA-AO-A1KR-01 TCGA-PL-A8LV-01 TCGA-AO-A1KT-01 TCGA-E2-A15H-01 TCGA-A8-A08O-01 TCGA-AN-A0AL-01 TCGA-E2-A15J-01 TCGA-E9-A244-01 TCGA-E9-A24A-01 TCGA-BH-A0B0-01 TCGA-A8-A093-01 TCGA-GM-A2DL-01 TCGA-S3-AA11-01 TCGA-EW-A1J6-01 TCGA-Z7-A8R5-01 TCGA-A7-A26H-01 TCGA-AQ-A54O-01 TCGA-BH-A1FC-01 TCGA-E9-A22B-01 TCGA-A2-A3XV-01 TCGA-BH-A0B9-01 TCGA-A8-A079-01 TCGA-E2-A15T-01 TCGA-AC-A6NO-01 TCGA-D8-A1JT-01 TCGA-D8-A1X7-01 TCGA-E9-A247-01 TCGA-A8-A07U-01 TCGA-XX-A899-01 TCGA-AO-A03U-01 TCGA-A8-A075-01 TCGA-D8-A73X-01 TCGA-BH-A18K-01 TCGA-B6-A1KI-01 TCGA-E9-A1R4-01 TCGA-BH-A0E1-01 TCGA-BH-A18S-01 TCGA-BH-A0DL-01 TCGA-A8-A08A-01 TCGA-EW-A423-01 TCGA-AN-A04A-01 TCGA-A1-A0SD-01 TCGA-EW-A1J2-01 TCGA-BH-A0GY-01 TCGA-C8-A12T-01 TCGA-W8-A86G-01 TCGA-A7-A5ZW-01 TCGA-E2-A158-01 TCGA-AR-A0TV-01 TCGA-E2-A56Z-01 TCGA-B6-A0IB-01 TCGA-C8-A1HF-01 TCGA-C8-A27B-01 TCGA-A8-A096-01 TCGA-A7-A13E-01 TCGA-BH-A0HA-01 TCGA-A2-A1G6-01 TCGA-A7-A26J-01 TCGA-A8-A094-01 TCGA-E2-A14O-01 TCGA-A2-A04Y-01 TCGA-AN-A0AS-01 TCGA-C8-A12X-01 TCGA-A7-A0D9-01 TCGA-BH-A204-01 TCGA-B6-A0WW-01 TCGA-BH-A0B4-01 TCGA-A7-A6VX-01 TCGA-AC-A3OD-01 TCGA-D8-A4Z1-01 TCGA-D8-A1XL-01 TCGA-E9-A5UO-01 TCGA-E2-A154-01 TCGA-AN-A0FV-01 TCGA-A8-A06R-01 TCGA-OL-A5RZ-01 TCGA-E2-A156-01 TCGA-A8-A07F-01 TCGA-AO-A0JJ-01 TCGA-E2-A1IK-01 TCGA-BH-A0C0-01 TCGA-AO-A1KP-01 TCGA-D8-A1JL-01 TCGA-A2-A3XZ-01 TCGA-B6-A0X7-01 TCGA-A8-A09I-01 TCGA-B6-A0RN-01 TCGA-OL-A5RV-01 TCGA-E2-A1BC-01 TCGA-A1-A0SP-01 TCGA-A2-A0YF-01 TCGA-A2-A3Y0-01 TCGA-AC-A3YI-01 TCGA-E9-A22D-01 TCGA-E2-A570-01 TCGA-A7-A0DB-01 TCGA-E2-A15F-01 TCGA-A1-A0SF-01 TCGA-EW-A6SD-01 TCGA-EW-A6SC-01 TCGA-A2-A0CX-01 TCGA-B6-A0RH-01 TCGA-AR-A1AU-01 TCGA-AO-A129-01 TCGA-BH-A6R8-01 TCGA-BH-A0W7-01 TCGA-D8-A1JP-01 TCGA-BH-A8FY-01 TCGA-A8-A09Z-01 TCGA-A8-A07W-01 TCGA-AO-A0JM-01 TCGA-E2-A15C-01 TCGA-E9-A229-01 TCGA-AR-A1AX-01 TCGA-V7-A7HQ-01 TCGA-D8-A27L-01 TCGA-E2-A14W-01 TCGA-AR-A0U3-01 TCGA-AO-A03R-01 TCGA-AN-A0FS-01 TCGA-E9-A1NF-01 TCGA-EW-A1PA-01 TCGA-AN-A046-01 TCGA-D8-A1X5-01 TCGA-D8-A27H-01 TCGA-A2-A0ER-01 TCGA-BH-A0BW-01 TCGA-E2-A14P-01 TCGA-C8-A12K-01 TCGA-A8-A09V-01 TCGA-EW-A1PG-01 TCGA-BH-A5J0-01 TCGA-AR-A1AW-01 TCGA-BH-A0HK-01 TCGA-AR-A24Z-01 TCGA-A1-A0SM-01 TCGA-AO-A124-01 TCGA-BH-A18V-01 TCGA-BH-A0BR-01 TCGA-Z7-A8R6-01 TCGA-OL-A66K-01 TCGA-D8-A1JC-01 TCGA-A8-A09D-01 TCGA-LD-A7W5-01 TCGA-E2-A1LA-01 TCGA-A2-A4S1-01 TCGA-AR-A256-01 TCGA-E9-A1NC-01 TCGA-A8-A095-01 TCGA-BH-A18U-01 TCGA-E9-A5FK-01 TCGA-D8-A1XB-01 TCGA-AN-A0XO-01 TCGA-BH-A0DQ-01 TCGA-BH-A0BL-01 TCGA-AR-A1AI-01 TCGA-AR-A250-01 TCGA-A2-A0T3-01 TCGA-OL-A5D8-01 TCGA-A2-A0YL-01 TCGA-A7-A5ZX-01 TCGA-C8-A137-01 TCGA-E9-A5FL-01 TCGA-E2-A14Z-01 TCGA-D8-A1JG-01 TCGA-AQ-A04H-01 TCGA-AR-A5QQ-01 TCGA-D8-A1XG-01 TCGA-B6-A0RS-01 TCGA-E2-A152-01 TCGA-S3-AA15-01 TCGA-AO-A03L-01 TCGA-B6-A0IJ-01 TCGA-C8-A1HN-01 TCGA-D8-A1J9-01 TCGA-A2-A0T0-01 TCGA-EW-A1OX-01 TCGA-AR-A24V-01 TCGA-AN-A0XS-01 TCGA-C8-A8HQ-01 TCGA-AO-A0J7-01 TCGA-OL-A66O-01 TCGA-BH-A1EV-01 TCGA-BH-A0HW-01 TCGA-A2-A0CR-01 TCGA-D8-A1XY-01 TCGA-A2-A0D1-01 TCGA-LL-A6FP-01 TCGA-E2-A1L8-01 TCGA-E2-A15M-01 TCGA-AN-A0FX-01 TCGA-B6-A0I5-01 TCGA-B6-A1KN-01 TCGA-AR-A24M-01 TCGA-BH-A18I-01 TCGA-A2-A1FW-01 TCGA-AO-A0JC-01 TCGA-A8-A083-01 TCGA-E2-A576-01 TCGA-GM-A3NW-01 TCGA-A8-A0A9-01 TCGA-A2-A04R-01 TCGA-AR-A2LQ-01 TCGA-BH-A0AZ-01 TCGA-AN-A0XW-01 TCGA-D8-A27E-01 TCGA-AC-A8OR-01 TCGA-E2-A573-01 TCGA-D8-A147-01 TCGA-A2-A04U-01 TCGA-A8-A0AB-01 TCGA-D8-A140-01 TCGA-LL-A5YN-01 TCGA-AR-A1AO-01 TCGA-A2-A3XU-01 TCGA-D8-A1XV-01 TCGA-AN-A04D-01 TCGA-AN-A0FT-01 TCGA-A8-A09B-01 TCGA-A2-A25B-01 TCGA-D8-A27W-01 TCGA-GM-A3XL-01 TCGA-C8-A275-01 TCGA-E9-A1RE-01 TCGA-C8-A3M8-01 TCGA-AN-A0XU-01 TCGA-A2-A3XW-01 TCGA-AN-A041-01 TCGA-AO-A03P-01 TCGA-BH-A0DS-01 TCGA-A2-A0EW-01 TCGA-D8-A1XU-01 TCGA-AO-A1KO-01 TCGA-D8-A1X6-01 TCGA-A7-A26I-01 TCGA-AQ-A7U7-01 TCGA-A1-A0SI-01 TCGA-A2-A25A-01 TCGA-PL-A8LX-01 TCGA-E9-A1RH-01 TCGA-A7-A0CH-01 TCGA-AO-A12E-01 TCGA-E2-A10A-01 TCGA-B6-A0RQ-01 TCGA-C8-A1HK-01 TCGA-E9-A1R5-01 TCGA-E9-A54Y-01 TCGA-E9-A243-01 TCGA-BH-A0HU-01 TCGA-E9-A2JS-01 TCGA-E2-A1IO-01 TCGA-OL-A5S0-01 TCGA-C8-A26Y-01 TCGA-A2-A25D-01 TCGA-EW-A1J3-01 TCGA-A2-A0EP-01 TCGA-BH-A1F8-01 TCGA-E2-A159-01 TCGA-C8-A12P-01 TCGA-A8-A0A7-01 TCGA-AN-A049-01 TCGA-E2-A14R-01 TCGA-B6-A0X5-01 TCGA-A2-A0YD-01 TCGA-A8-A086-01 TCGA-BH-A0AW-01 TCGA-A2-A04X-01 TCGA-D8-A27F-01 TCGA-A7-A0CD-01 TCGA-A8-A07J-01 TCGA-AN-A0FJ-01 TCGA-D8-A1JK-01 TCGA-EW-A1P3-01 TCGA-B6-A0WV-01 TCGA-BH-A18R-01 TCGA-E2-A1LI-01 TCGA-C8-A12N-01 TCGA-A2-A0SX-01 TCGA-GM-A5PX-01 TCGA-BH-A1FD-01 TCGA-BH-A0BF-01 TCGA-AR-A5QN-01 TCGA-UL-AAZ6-01 TCGA-B6-A0RG-01 TCGA-BH-A0B5-01 TCGA-BH-A0DD-01 TCGA-B6-A0RE-01 TCGA-E2-A1LH-01 TCGA-EW-A1IX-01 TCGA-BH-A1F6-01 TCGA-BH-A0HX-01 TCGA-C8-A138-01 TCGA-E2-A14N-01 TCGA-BH-A1FH-01 TCGA-A2-A259-01 TCGA-BH-A0DO-01 TCGA-GM-A2DD-01 TCGA-E2-A1B1-01 TCGA-AN-A0FF-01 TCGA-5T-A9QA-01 TCGA-D8-A27N-01 TCGA-D8-A1X9-01 TCGA-A8-A06Z-01 TCGA-OL-A5RW-01 TCGA-AR-A0TR-01 TCGA-A8-A099-01 TCGA-E9-A1RC-01 TCGA-LL-A8F5-01 TCGA-OL-A5RX-01 TCGA-A8-A092-01 TCGA-HN-A2NL-01 TCGA-AC-A23C-01 TCGA-E9-A1NE-01 TCGA-A7-A56D-01 TCGA-AC-A3QP-01 TCGA-GM-A2DH-01 TCGA-A8-A09M-01 TCGA-EW-A1PH-01 TCGA-BH-A6R9-01 TCGA-C8-A8HP-01 TCGA-A1-A0SH-01 TCGA-AR-A24X-01 TCGA-BH-A0C7-01 TCGA-A1-A0SB-01 TCGA-D8-A73W-01 TCGA-D8-A1Y0-01 TCGA-A2-A04V-01 TCGA-B6-A0IO-01 TCGA-BH-A18Q-01 TCGA-AC-A2B8-01 TCGA-A8-A09A-01 TCGA-LL-A6FQ-01 TCGA-BH-A1FM-01 TCGA-AR-A24R-01 TCGA-AR-A251-01 TCGA-AO-A12B-01 TCGA-BH-A202-01 TCGA-A2-A0ES-01 TCGA-AO-A0JF-01 TCGA-BH-A0DH-01 TCGA-E2-A14T-01 TCGA-D8-A1JN-01 TCGA-EW-A1OV-01 TCGA-E2-A1IE-01 TCGA-D8-A1JE-01 TCGA-AR-A1AR-01 TCGA-A1-A0SN-01 TCGA-E9-A295-01 TCGA-A8-A08I-01 TCGA-BH-A0HP-01 TCGA-E2-A1IU-01 TCGA-BH-A0BS-01 TCGA-EW-A1P8-01 TCGA-A8-A06Y-01 TCGA-GI-A2C8-01 TCGA-AR-A24P-01 TCGA-EW-A1P7-01 TCGA-OL-A5RY-01 TCGA-B6-A0RP-01 TCGA-C8-A12Z-01 TCGA-A8-A097-01 TCGA-E9-A22H-01 TCGA-D8-A3Z6-01 TCGA-E2-A155-01 TCGA-AR-A2LK-01 TCGA-A8-A08J-01 TCGA-B6-A409-01 TCGA-B6-A0X1-01 TCGA-A7-A26F-01 TCGA-B6-A0IG-01 TCGA-E2-A15D-01 TCGA-A8-A090-01 TCGA-E9-A1RB-01 TCGA-E9-A248-01 TCGA-BH-A0E7-01 TCGA-AO-A12F-01 TCGA-AN-A0AJ-01 TCGA-D8-A27V-01 TCGA-EW-A1P4-01 TCGA-AO-A12D-01 TCGA-AO-A128-01 TCGA-AR-A24T-01 TCGA-E2-A1B6-01 TCGA-EW-A1P6-01 TCGA-E9-A228-01 TCGA-GM-A2DF-01 TCGA-D8-A1XF-01 TCGA-BH-A18F-01 TCGA-E2-A14X-01 TCGA-E9-A1N4-01 TCGA-A2-A0CT-01 TCGA-E9-A1RG-01 TCGA-BH-A1F2-01 TCGA-E9-A1N9-01 TCGA-B6-A0I9-01 TCGA-GM-A2DM-01 TCGA-AC-A5XU-01 TCGA-A2-A0YG-01 TCGA-S3-A6ZH-01 TCGA-A8-A09Q-01 TCGA-A2-A0T4-01 TCGA-AC-A2FF-01 TCGA-C8-A12V-01 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TCGA-BH-A0B3-01 TCGA-D8-A1JS-01 TCGA-B6-A40B-01 TCGA-B6-A0X0-01 TCGA-D8-A145-01 TCGA-WT-AB44-01 TCGA-BH-A1FR-01 TCGA-A2-A0CW-01 TCGA-A7-A425-01 TCGA-B6-A0IK-01 TCGA-A2-A0CU-01 TCGA-C8-A8HR-01 TCGA-E9-A1RF-01 TCGA-AN-A0FD-01 TCGA-BH-A18G-01 TCGA-LL-A73Z-01 TCGA-E2-A15E-01 TCGA-E2-A1L7-01 TCGA-A8-A07P-01 TCGA-A2-A0YE-01 TCGA-A8-A08B-01 TCGA-D8-A1XR-01 TCGA-BH-A8FZ-01 TCGA-S3-AA17-01 TCGA-B6-A0IH-01 TCGA-AO-A0J2-01 TCGA-AR-A1AL-01 TCGA-EW-A1IZ-01 TCGA-C8-A12W-01 TCGA-BH-A1EO-01 TCGA-A8-A09G-01 TCGA-D8-A13Z-01 TCGA-D8-A27K-01 TCGA-BH-A28Q-01 TCGA-EW-A1J1-01 TCGA-AO-A03O-01 TCGA-C8-A1HG-01 TCGA-D8-A1XK-01 TCGA-C8-A1HI-01 TCGA-3C-AAAU-01 TCGA-AO-A0J4-01 TCGA-B6-A0IM-01 TCGA-AC-A8OQ-01 TCGA-A2-A0EN-01 TCGA-EW-A1PB-01 TCGA-D8-A1JU-01 TCGA-C8-A12L-01 TCGA-E2-A108-01 TCGA-BH-A0BT-01 TCGA-A2-A0YK-01 TCGA-E9-A1N8-01 TCGA-A8-A085-01 TCGA-LL-A7T0-01 TCGA-E2-A574-01 TCGA-A1-A0SO-01 TCGA-BH-A0DI-01 TCGA-E2-A1IG-01 TCGA-B6-A0IA-01 TCGA-E9-A1NH-01 TCGA-EW-A6SA-01 TCGA-BH-A0C3-01 TCGA-BH-A1F0-01 TCGA-A8-A06Q-01 TCGA-BH-A0GZ-01 TCGA-AR-A0U0-01
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initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_log2CNA.txt
ADDED
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+
cancer_study_identifier: brca_tcga_pan_can_atlas_2018
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| 2 |
+
stable_id: brca_tcga_pan_can_atlas_2018_log2CNA
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| 3 |
+
case_list_name: Samples with log2 copy-number data
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| 4 |
+
case_list_description: Samples with log2 copy-number data (1070 samples)
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| 5 |
+
case_list_category: all_cases_with_log2_cna_data
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| 6 |
+
case_list_ids: TCGA-OL-A66H-01 TCGA-3C-AALK-01 TCGA-AR-A1AH-01 TCGA-AC-A5EH-01 TCGA-EW-A2FW-01 TCGA-E9-A1R0-01 TCGA-B6-A2IU-01 TCGA-AR-A1AJ-01 TCGA-A7-A13G-01 TCGA-AC-A62Y-01 TCGA-E9-A1QZ-01 TCGA-E9-A1R2-01 TCGA-E9-A3X8-01 TCGA-AR-A255-01 TCGA-E2-A10B-01 TCGA-AO-A0JD-01 TCGA-EW-A2FS-01 TCGA-D8-A1XA-01 TCGA-AO-A1KQ-01 TCGA-A8-A0A6-01 TCGA-A7-A3RF-01 TCGA-A7-A3IY-01 TCGA-B6-A0IE-01 TCGA-GM-A2D9-01 TCGA-D8-A3Z5-01 TCGA-E9-A1ND-01 TCGA-AN-A03X-01 TCGA-AQ-A04J-01 TCGA-B6-A0RO-01 TCGA-E9-A1NA-01 TCGA-AC-A7VC-01 TCGA-LD-A66U-01 TCGA-AO-A0J8-01 TCGA-A8-A08R-01 TCGA-BH-A0DZ-01 TCGA-EW-A1PD-01 TCGA-E9-A1N5-01 TCGA-A8-A07B-01 TCGA-D8-A1J8-01 TCGA-B6-A0RV-01 TCGA-E2-A15R-01 TCGA-A8-A07O-01 TCGA-E9-A3QA-01 TCGA-BH-A2L8-01 TCGA-A7-A0CE-01 TCGA-BH-A0H0-01 TCGA-A2-A3XX-01 TCGA-AC-A2FB-01 TCGA-A2-A0D4-01 TCGA-A2-A0YC-01 TCGA-GM-A2DK-01 TCGA-GM-A2DC-01 TCGA-A2-A0YH-01 TCGA-AR-A24N-01 TCGA-A7-A6VV-01 TCGA-E2-A1B0-01 TCGA-BH-A1EY-01 TCGA-EW-A6S9-01 TCGA-A2-A0CQ-01 TCGA-AC-A8OS-01 TCGA-GM-A2DN-01 TCGA-AO-A03M-01 TCGA-A2-A3XT-01 TCGA-A7-A4SE-01 TCGA-BH-A0DT-01 TCGA-AC-A6IV-01 TCGA-LL-A7SZ-01 TCGA-A1-A0SJ-01 TCGA-AR-A2LJ-01 TCGA-AQ-A1H3-01 TCGA-D8-A1JB-01 TCGA-B6-A0IQ-01 TCGA-BH-A0BC-01 TCGA-BH-A1EW-01 TCGA-AO-A1KS-01 TCGA-BH-A1FG-01 TCGA-AR-A0TS-01 TCGA-C8-A1HL-01 TCGA-AO-A03T-01 TCGA-D8-A27P-01 TCGA-D8-A1JD-01 TCGA-E2-A1IL-01 TCGA-A7-A3IZ-01 TCGA-A2-A0CM-01 TCGA-AN-A04C-01 TCGA-OL-A66J-01 TCGA-AR-A2LO-01 TCGA-A8-A08L-01 TCGA-BH-A201-01 TCGA-LL-A5YM-01 TCGA-AC-A4ZE-01 TCGA-A2-A0T2-01 TCGA-A8-A06X-01 TCGA-AC-A3W5-01 TCGA-D8-A143-01 TCGA-AR-A0TP-01 TCGA-C8-A134-01 TCGA-AR-A0TZ-01 TCGA-A2-A0D2-01 TCGA-EW-A1P0-01 TCGA-A2-A4RW-01 TCGA-A2-A1G0-01 TCGA-AR-A24H-01 TCGA-D8-A1XV-01 TCGA-A8-A09B-01 TCGA-D8-A13Y-01 TCGA-AC-A2FG-01 TCGA-S3-AA15-01 TCGA-C8-A12Y-01 TCGA-A8-A07L-01 TCGA-A2-A0YT-01 TCGA-A8-A07I-01 TCGA-D8-A1JI-01 TCGA-E2-A15P-01 TCGA-A8-A06T-01 TCGA-UU-A93S-01 TCGA-B6-A0RL-01 TCGA-E9-A1R6-01 TCGA-A2-A0EY-01 TCGA-D8-A1XZ-01 TCGA-AC-A2FE-01 TCGA-BH-A0H3-01 TCGA-XX-A89A-01 TCGA-EW-A1OY-01 TCGA-A8-A08X-01 TCGA-AR-A0TY-01 TCGA-A2-A0SY-01 TCGA-LL-A9Q3-01 TCGA-A1-A0SQ-01 TCGA-AR-A5QM-01 TCGA-A2-A0SW-01 TCGA-EW-A1P5-01 TCGA-PE-A5DE-01 TCGA-BH-A18N-01 TCGA-E9-A1RD-01 TCGA-AC-A23H-01 TCGA-AC-A2BM-01 TCGA-BH-A0WA-01 TCGA-BH-A42T-01 TCGA-AN-A0FW-01 TCGA-B6-A40C-01 TCGA-BH-A0EA-01 TCGA-A2-A1FZ-01 TCGA-C8-A12Q-01 TCGA-B6-A400-01 TCGA-BH-A0BA-01 TCGA-BH-AB28-01 TCGA-A8-A09N-01 TCGA-E2-A2P6-01 TCGA-B6-A0RT-01 TCGA-AR-A1AY-01 TCGA-A2-A25C-01 TCGA-S3-AA10-01 TCGA-OL-A5DA-01 TCGA-D8-A27R-01 TCGA-E2-A15A-01 TCGA-A7-A5ZV-01 TCGA-LL-A50Y-01 TCGA-B6-A0WX-01 TCGA-BH-A1EN-01 TCGA-C8-A26Z-01 TCGA-A2-A04Q-01 TCGA-E2-A14Y-01 TCGA-BH-A1FN-01 TCGA-BH-A0E0-01 TCGA-E9-A2JT-01 TCGA-OL-A5D6-01 TCGA-AR-A0U1-01 TCGA-A2-A4S3-01 TCGA-E2-A15G-01 TCGA-AO-A0J9-01 TCGA-C8-A12U-01 TCGA-A8-A09X-01 TCGA-BH-A0HQ-01 TCGA-A8-A07E-01 TCGA-A1-A0SE-01 TCGA-A8-A09R-01 TCGA-E2-A107-01 TCGA-E9-A3HO-01 TCGA-A8-A091-01 TCGA-A8-A076-01 TCGA-D8-A1XT-01 TCGA-AR-A1AQ-01 TCGA-AR-A24U-01 TCGA-BH-A42V-01 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TCGA-A2-A0YK-01 TCGA-E9-A1N8-01 TCGA-A8-A085-01 TCGA-AN-A0FZ-01 TCGA-B6-A402-01 TCGA-A1-A0SO-01 TCGA-BH-A0DI-01 TCGA-E2-A1IG-01 TCGA-EW-A6SC-01 TCGA-B6-A0IA-01 TCGA-E9-A1NH-01 TCGA-EW-A6SA-01 TCGA-BH-A0C3-01 TCGA-BH-A1F0-01 TCGA-A8-A06Q-01 TCGA-BH-A0GZ-01 TCGA-AR-A0U0-01
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initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_methylation_all.txt
ADDED
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cancer_study_identifier: brca_tcga_pan_can_atlas_2018
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| 2 |
+
stable_id: brca_tcga_pan_can_atlas_2018_methylation_all
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| 3 |
+
case_list_name: Samples with methylation data
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| 4 |
+
case_list_description: Samples with methylation data (1066 samples)
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| 5 |
+
case_list_category: all_cases_with_methylation_data
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| 6 |
+
case_list_ids: TCGA-3C-AAAU-01 TCGA-3C-AALI-01 TCGA-3C-AALJ-01 TCGA-3C-AALK-01 TCGA-4H-AAAK-01 TCGA-5L-AAT0-01 TCGA-5T-A9QA-01 TCGA-A1-A0SB-01 TCGA-A1-A0SD-01 TCGA-A1-A0SE-01 TCGA-A1-A0SF-01 TCGA-A1-A0SG-01 TCGA-A1-A0SH-01 TCGA-A1-A0SI-01 TCGA-A1-A0SJ-01 TCGA-A1-A0SK-01 TCGA-A1-A0SM-01 TCGA-A1-A0SN-01 TCGA-A1-A0SO-01 TCGA-A1-A0SP-01 TCGA-A1-A0SQ-01 TCGA-A2-A04N-01 TCGA-A2-A04P-01 TCGA-A2-A04Q-01 TCGA-A2-A04R-01 TCGA-A2-A04T-01 TCGA-A2-A04U-01 TCGA-A2-A04V-01 TCGA-A2-A04W-01 TCGA-A2-A04X-01 TCGA-A2-A04Y-01 TCGA-A2-A0CK-01 TCGA-A2-A0CL-01 TCGA-A2-A0CM-01 TCGA-A2-A0CO-01 TCGA-A2-A0CP-01 TCGA-A2-A0CQ-01 TCGA-A2-A0CR-01 TCGA-A2-A0CS-01 TCGA-A2-A0CT-01 TCGA-A2-A0CU-01 TCGA-A2-A0CV-01 TCGA-A2-A0CW-01 TCGA-A2-A0CX-01 TCGA-A2-A0CZ-01 TCGA-A2-A0D0-01 TCGA-A2-A0D1-01 TCGA-A2-A0D2-01 TCGA-A2-A0D3-01 TCGA-A2-A0D4-01 TCGA-A2-A0EM-01 TCGA-A2-A0EN-01 TCGA-A2-A0EO-01 TCGA-A2-A0EP-01 TCGA-A2-A0EQ-01 TCGA-A2-A0ER-01 TCGA-A2-A0ES-01 TCGA-A2-A0ET-01 TCGA-A2-A0EU-01 TCGA-A2-A0EV-01 TCGA-A2-A0EW-01 TCGA-A2-A0EX-01 TCGA-A2-A0EY-01 TCGA-A2-A0ST-01 TCGA-A2-A0SU-01 TCGA-A2-A0SV-01 TCGA-A2-A0SW-01 TCGA-A2-A0SX-01 TCGA-A2-A0SY-01 TCGA-A2-A0T0-01 TCGA-A2-A0T1-01 TCGA-A2-A0T2-01 TCGA-A2-A0T3-01 TCGA-A2-A0T4-01 TCGA-A2-A0T5-01 TCGA-A2-A0T6-01 TCGA-A2-A0T7-01 TCGA-A2-A0YC-01 TCGA-A2-A0YD-01 TCGA-A2-A0YE-01 TCGA-A2-A0YF-01 TCGA-A2-A0YG-01 TCGA-A2-A0YH-01 TCGA-A2-A0YI-01 TCGA-A2-A0YJ-01 TCGA-A2-A0YK-01 TCGA-A2-A0YL-01 TCGA-A2-A0YM-01 TCGA-A2-A0YT-01 TCGA-A2-A1FV-01 TCGA-A2-A1FW-01 TCGA-A2-A1FX-01 TCGA-A2-A1FZ-01 TCGA-A2-A1G0-01 TCGA-A2-A1G1-01 TCGA-A2-A1G4-01 TCGA-A2-A1G6-01 TCGA-A2-A259-01 TCGA-A2-A25A-01 TCGA-A2-A25B-01 TCGA-A2-A25C-01 TCGA-A2-A25D-01 TCGA-A2-A25E-01 TCGA-A2-A25F-01 TCGA-A2-A3KC-01 TCGA-A2-A3KD-01 TCGA-A2-A3XS-01 TCGA-A2-A3XT-01 TCGA-A2-A3XU-01 TCGA-A2-A3XV-01 TCGA-A2-A3XW-01 TCGA-A2-A3XX-01 TCGA-A2-A3XY-01 TCGA-A2-A3XZ-01 TCGA-A2-A3Y0-01 TCGA-A2-A4RW-01 TCGA-A2-A4RX-01 TCGA-A2-A4RY-01 TCGA-A2-A4S0-01 TCGA-A2-A4S1-01 TCGA-A2-A4S2-01 TCGA-A2-A4S3-01 TCGA-A7-A0CD-01 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TCGA-S3-AA14-01 TCGA-S3-AA15-01 TCGA-S3-AA17-01 TCGA-UL-AAZ6-01 TCGA-UU-A93S-01 TCGA-V7-A7HQ-01 TCGA-W8-A86G-01 TCGA-WT-AB41-01 TCGA-WT-AB44-01 TCGA-XX-A899-01 TCGA-XX-A89A-01 TCGA-Z7-A8R5-01 TCGA-Z7-A8R6-01
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initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_methylation_hm450.txt
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cancer_study_identifier: brca_tcga_pan_can_atlas_2018
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| 2 |
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stable_id: brca_tcga_pan_can_atlas_2018_methylation_hm450
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case_list_name: Samples with methylation data (HM450)
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case_list_description: Samples with methylation (HM450) data (779 samples)
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case_list_category: all_cases_with_methylation_data
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| 6 |
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case_list_ids: TCGA-3C-AAAU-01 TCGA-3C-AALI-01 TCGA-3C-AALJ-01 TCGA-3C-AALK-01 TCGA-4H-AAAK-01 TCGA-5L-AAT0-01 TCGA-5T-A9QA-01 TCGA-A1-A0SB-01 TCGA-A1-A0SE-01 TCGA-A1-A0SF-01 TCGA-A1-A0SG-01 TCGA-A1-A0SH-01 TCGA-A1-A0SI-01 TCGA-A1-A0SJ-01 TCGA-A1-A0SK-01 TCGA-A1-A0SM-01 TCGA-A1-A0SN-01 TCGA-A1-A0SO-01 TCGA-A1-A0SP-01 TCGA-A1-A0SQ-01 TCGA-A2-A04R-01 TCGA-A2-A0CK-01 TCGA-A2-A0CO-01 TCGA-A2-A0CR-01 TCGA-A2-A0CT-01 TCGA-A2-A0EN-01 TCGA-A2-A0EP-01 TCGA-A2-A0EU-01 TCGA-A2-A0ST-01 TCGA-A2-A0SU-01 TCGA-A2-A0SV-01 TCGA-A2-A0SW-01 TCGA-A2-A0SX-01 TCGA-A2-A0SY-01 TCGA-A2-A0T0-01 TCGA-A2-A0T1-01 TCGA-A2-A0T2-01 TCGA-A2-A0T4-01 TCGA-A2-A0T5-01 TCGA-A2-A0T6-01 TCGA-A2-A0T7-01 TCGA-A2-A0YC-01 TCGA-A2-A0YD-01 TCGA-A2-A0YE-01 TCGA-A2-A0YF-01 TCGA-A2-A0YG-01 TCGA-A2-A0YH-01 TCGA-A2-A0YI-01 TCGA-A2-A0YJ-01 TCGA-A2-A0YK-01 TCGA-A2-A0YL-01 TCGA-A2-A0YM-01 TCGA-A2-A0YT-01 TCGA-A2-A1FV-01 TCGA-A2-A1FW-01 TCGA-A2-A1FX-01 TCGA-A2-A1FZ-01 TCGA-A2-A1G0-01 TCGA-A2-A1G1-01 TCGA-A2-A1G4-01 TCGA-A2-A1G6-01 TCGA-A2-A259-01 TCGA-A2-A25A-01 TCGA-A2-A25B-01 TCGA-A2-A25C-01 TCGA-A2-A25D-01 TCGA-A2-A25E-01 TCGA-A2-A25F-01 TCGA-A2-A3KC-01 TCGA-A2-A3KD-01 TCGA-A2-A3XS-01 TCGA-A2-A3XT-01 TCGA-A2-A3XU-01 TCGA-A2-A3XV-01 TCGA-A2-A3XW-01 TCGA-A2-A3XX-01 TCGA-A2-A3XY-01 TCGA-A2-A3XZ-01 TCGA-A2-A3Y0-01 TCGA-A2-A4RW-01 TCGA-A2-A4RX-01 TCGA-A2-A4RY-01 TCGA-A2-A4S0-01 TCGA-A2-A4S1-01 TCGA-A2-A4S2-01 TCGA-A2-A4S3-01 TCGA-A7-A0D9-01 TCGA-A7-A13D-01 TCGA-A7-A13E-01 TCGA-A7-A13F-01 TCGA-A7-A13G-01 TCGA-A7-A13H-01 TCGA-A7-A26E-01 TCGA-A7-A26E-01 TCGA-A7-A26F-01 TCGA-A7-A26G-01 TCGA-A7-A26H-01 TCGA-A7-A26I-01 TCGA-A7-A26J-01 TCGA-A7-A26J-01 TCGA-A7-A2KD-01 TCGA-A7-A3IY-01 TCGA-A7-A3IZ-01 TCGA-A7-A3J0-01 TCGA-A7-A3J1-01 TCGA-A7-A3RF-01 TCGA-A7-A425-01 TCGA-A7-A426-01 TCGA-A7-A4SA-01 TCGA-A7-A4SB-01 TCGA-A7-A4SC-01 TCGA-A7-A4SD-01 TCGA-A7-A4SE-01 TCGA-A7-A4SF-01 TCGA-A7-A56D-01 TCGA-A7-A5ZV-01 TCGA-A7-A5ZW-01 TCGA-A7-A5ZX-01 TCGA-A7-A6VV-01 TCGA-A7-A6VW-01 TCGA-A7-A6VX-01 TCGA-A7-A6VY-01 TCGA-A8-A075-01 TCGA-A8-A08O-01 TCGA-A8-A0A6-01 TCGA-A8-A0AD-01 TCGA-AC-A23C-01 TCGA-AC-A23E-01 TCGA-AC-A23G-01 TCGA-AC-A23H-01 TCGA-AC-A2B8-01 TCGA-AC-A2BK-01 TCGA-AC-A2BM-01 TCGA-AC-A2FB-01 TCGA-AC-A2FE-01 TCGA-AC-A2FF-01 TCGA-AC-A2FG-01 TCGA-AC-A2FK-01 TCGA-AC-A2FM-01 TCGA-AC-A2FO-01 TCGA-AC-A2QH-01 TCGA-AC-A2QI-01 TCGA-AC-A2QJ-01 TCGA-AC-A3BB-01 TCGA-AC-A3EH-01 TCGA-AC-A3HN-01 TCGA-AC-A3OD-01 TCGA-AC-A3QP-01 TCGA-AC-A3QQ-01 TCGA-AC-A3TM-01 TCGA-AC-A3TN-01 TCGA-AC-A3W5-01 TCGA-AC-A3W6-01 TCGA-AC-A3W7-01 TCGA-AC-A3YI-01 TCGA-AC-A3YJ-01 TCGA-AC-A4ZE-01 TCGA-AC-A5EH-01 TCGA-AC-A5EI-01 TCGA-AC-A5XS-01 TCGA-AC-A5XU-01 TCGA-AC-A62V-01 TCGA-AC-A62X-01 TCGA-AC-A62Y-01 TCGA-AC-A6IV-01 TCGA-AC-A6IW-01 TCGA-AC-A6IX-01 TCGA-AC-A6NO-01 TCGA-AC-A7VB-01 TCGA-AC-A7VC-01 TCGA-AC-A8OP-01 TCGA-AC-A8OQ-01 TCGA-AC-A8OR-01 TCGA-AC-A8OS-01 TCGA-AN-A0XL-01 TCGA-AN-A0XN-01 TCGA-AN-A0XO-01 TCGA-AN-A0XP-01 TCGA-AN-A0XR-01 TCGA-AN-A0XS-01 TCGA-AN-A0XT-01 TCGA-AN-A0XU-01 TCGA-AN-A0XV-01 TCGA-AN-A0XW-01 TCGA-AO-A03L-01 TCGA-AO-A03M-01 TCGA-AO-A03N-01 TCGA-AO-A03U-01 TCGA-AO-A0JA-01 TCGA-AO-A0JB-01 TCGA-AO-A0JC-01 TCGA-AO-A0JD-01 TCGA-AO-A0JE-01 TCGA-AO-A0JF-01 TCGA-AO-A0JG-01 TCGA-AO-A0JI-01 TCGA-AO-A0JJ-01 TCGA-AO-A0JL-01 TCGA-AO-A0JM-01 TCGA-AO-A124-01 TCGA-AO-A125-01 TCGA-AO-A126-01 TCGA-AO-A128-01 TCGA-AO-A129-01 TCGA-AO-A12B-01 TCGA-AO-A12E-01 TCGA-AO-A12G-01 TCGA-AO-A1KO-01 TCGA-AO-A1KP-01 TCGA-AO-A1KQ-01 TCGA-AO-A1KR-01 TCGA-AO-A1KS-01 TCGA-AO-A1KT-01 TCGA-AQ-A04H-01 TCGA-AQ-A04L-01 TCGA-AQ-A0Y5-01 TCGA-AQ-A1H2-01 TCGA-AQ-A1H3-01 TCGA-AQ-A54N-01 TCGA-AQ-A54O-01 TCGA-AQ-A7U7-01 TCGA-AR-A0TP-01 TCGA-AR-A0TQ-01 TCGA-AR-A0TR-01 TCGA-AR-A0TT-01 TCGA-AR-A0TU-01 TCGA-AR-A0TV-01 TCGA-AR-A0TW-01 TCGA-AR-A0TX-01 TCGA-AR-A0TZ-01 TCGA-AR-A0U0-01 TCGA-AR-A0U2-01 TCGA-AR-A0U3-01 TCGA-AR-A0U4-01 TCGA-AR-A1AI-01 TCGA-AR-A1AJ-01 TCGA-AR-A1AK-01 TCGA-AR-A1AL-01 TCGA-AR-A1AM-01 TCGA-AR-A1AN-01 TCGA-AR-A1AO-01 TCGA-AR-A1AP-01 TCGA-AR-A1AQ-01 TCGA-AR-A1AR-01 TCGA-AR-A1AS-01 TCGA-AR-A1AT-01 TCGA-AR-A1AU-01 TCGA-AR-A1AV-01 TCGA-AR-A1AW-01 TCGA-AR-A1AX-01 TCGA-AR-A1AY-01 TCGA-AR-A24H-01 TCGA-AR-A24K-01 TCGA-AR-A24L-01 TCGA-AR-A24M-01 TCGA-AR-A24N-01 TCGA-AR-A24O-01 TCGA-AR-A24P-01 TCGA-AR-A24Q-01 TCGA-AR-A24R-01 TCGA-AR-A24S-01 TCGA-AR-A24T-01 TCGA-AR-A24U-01 TCGA-AR-A24V-01 TCGA-AR-A24W-01 TCGA-AR-A24X-01 TCGA-AR-A24Z-01 TCGA-AR-A250-01 TCGA-AR-A251-01 TCGA-AR-A252-01 TCGA-AR-A254-01 TCGA-AR-A255-01 TCGA-AR-A256-01 TCGA-AR-A2LE-01 TCGA-AR-A2LH-01 TCGA-AR-A2LJ-01 TCGA-AR-A2LK-01 TCGA-AR-A2LM-01 TCGA-AR-A2LN-01 TCGA-AR-A2LO-01 TCGA-AR-A2LQ-01 TCGA-AR-A5QM-01 TCGA-AR-A5QN-01 TCGA-AR-A5QP-01 TCGA-AR-A5QQ-01 TCGA-B6-A0I1-01 TCGA-B6-A0IK-01 TCGA-B6-A0RE-01 TCGA-B6-A0RG-01 TCGA-B6-A0RI-01 TCGA-B6-A0RL-01 TCGA-B6-A0RM-01 TCGA-B6-A0RN-01 TCGA-B6-A0RO-01 TCGA-B6-A0RP-01 TCGA-B6-A0RS-01 TCGA-B6-A0RT-01 TCGA-B6-A0RU-01 TCGA-B6-A0RV-01 TCGA-B6-A0WT-01 TCGA-B6-A0WV-01 TCGA-B6-A0WW-01 TCGA-B6-A0WX-01 TCGA-B6-A0WY-01 TCGA-B6-A0WZ-01 TCGA-B6-A0X1-01 TCGA-B6-A0X4-01 TCGA-B6-A0X5-01 TCGA-B6-A0X7-01 TCGA-B6-A1KC-01 TCGA-B6-A1KC-01 TCGA-B6-A1KF-01 TCGA-B6-A1KI-01 TCGA-B6-A1KN-01 TCGA-B6-A2IU-01 TCGA-B6-A3ZX-01 TCGA-B6-A400-01 TCGA-B6-A401-01 TCGA-B6-A402-01 TCGA-B6-A408-01 TCGA-B6-A409-01 TCGA-B6-A40B-01 TCGA-B6-A40C-01 TCGA-BH-A0AU-01 TCGA-BH-A0AW-01 TCGA-BH-A0AZ-01 TCGA-BH-A0B2-01 TCGA-BH-A0B3-01 TCGA-BH-A0B5-01 TCGA-BH-A0B8-01 TCGA-BH-A0B9-01 TCGA-BH-A0BA-01 TCGA-BH-A0BC-01 TCGA-BH-A0BF-01 TCGA-BH-A0BJ-01 TCGA-BH-A0BM-01 TCGA-BH-A0BS-01 TCGA-BH-A0BT-01 TCGA-BH-A0BZ-01 TCGA-BH-A0C0-01 TCGA-BH-A0C3-01 TCGA-BH-A0DD-01 TCGA-BH-A0DG-01 TCGA-BH-A0DH-01 TCGA-BH-A0DI-01 TCGA-BH-A0DK-01 TCGA-BH-A0DP-01 TCGA-BH-A0DQ-01 TCGA-BH-A0DS-01 TCGA-BH-A0DV-01 TCGA-BH-A0E0-01 TCGA-BH-A0E1-01 TCGA-BH-A0E2-01 TCGA-BH-A0GY-01 TCGA-BH-A0GZ-01 TCGA-BH-A0H0-01 TCGA-BH-A0H3-01 TCGA-BH-A0H6-01 TCGA-BH-A0H7-01 TCGA-BH-A0H9-01 TCGA-BH-A0HA-01 TCGA-BH-A0HB-01 TCGA-BH-A0HF-01 TCGA-BH-A0HI-01 TCGA-BH-A0HK-01 TCGA-BH-A0HN-01 TCGA-BH-A0HP-01 TCGA-BH-A0HX-01 TCGA-BH-A0HY-01 TCGA-BH-A0RX-01 TCGA-BH-A0W3-01 TCGA-BH-A0W4-01 TCGA-BH-A0W5-01 TCGA-BH-A0WA-01 TCGA-BH-A1EN-01 TCGA-BH-A1EO-01 TCGA-BH-A1ES-01 TCGA-BH-A1ET-01 TCGA-BH-A1EU-01 TCGA-BH-A1EV-01 TCGA-BH-A1EW-01 TCGA-BH-A1EX-01 TCGA-BH-A1EY-01 TCGA-BH-A1F0-01 TCGA-BH-A1F2-01 TCGA-BH-A1F5-01 TCGA-BH-A1F6-01 TCGA-BH-A1F8-01 TCGA-BH-A1FB-01 TCGA-BH-A1FC-01 TCGA-BH-A1FD-01 TCGA-BH-A1FE-01 TCGA-BH-A1FG-01 TCGA-BH-A1FH-01 TCGA-BH-A1FJ-01 TCGA-BH-A1FL-01 TCGA-BH-A1FM-01 TCGA-BH-A1FN-01 TCGA-BH-A1FR-01 TCGA-BH-A1FU-01 TCGA-BH-A201-01 TCGA-BH-A202-01 TCGA-BH-A203-01 TCGA-BH-A204-01 TCGA-BH-A208-01 TCGA-BH-A209-01 TCGA-BH-A28O-01 TCGA-BH-A28Q-01 TCGA-BH-A2L8-01 TCGA-BH-A42T-01 TCGA-BH-A42U-01 TCGA-BH-A42V-01 TCGA-BH-A5IZ-01 TCGA-BH-A5J0-01 TCGA-BH-A6R8-01 TCGA-BH-A6R9-01 TCGA-BH-A8FY-01 TCGA-BH-A8FZ-01 TCGA-BH-A8G0-01 TCGA-BH-AB28-01 TCGA-C8-A1HE-01 TCGA-C8-A1HF-01 TCGA-C8-A1HG-01 TCGA-C8-A1HI-01 TCGA-C8-A1HJ-01 TCGA-C8-A1HK-01 TCGA-C8-A1HL-01 TCGA-C8-A1HM-01 TCGA-C8-A1HN-01 TCGA-C8-A1HO-01 TCGA-C8-A26V-01 TCGA-C8-A26W-01 TCGA-C8-A26X-01 TCGA-C8-A26Y-01 TCGA-C8-A26Z-01 TCGA-C8-A273-01 TCGA-C8-A274-01 TCGA-C8-A275-01 TCGA-C8-A278-01 TCGA-C8-A27A-01 TCGA-C8-A27B-01 TCGA-C8-A3M7-01 TCGA-C8-A3M8-01 TCGA-C8-A8HP-01 TCGA-C8-A8HQ-01 TCGA-C8-A8HR-01 TCGA-C8-A9FZ-01 TCGA-D8-A1J8-01 TCGA-D8-A1J9-01 TCGA-D8-A1JA-01 TCGA-D8-A1JB-01 TCGA-D8-A1JC-01 TCGA-D8-A1JD-01 TCGA-D8-A1JE-01 TCGA-D8-A1JF-01 TCGA-D8-A1JG-01 TCGA-D8-A1JH-01 TCGA-D8-A1JI-01 TCGA-D8-A1JJ-01 TCGA-D8-A1JK-01 TCGA-D8-A1JL-01 TCGA-D8-A1JM-01 TCGA-D8-A1JN-01 TCGA-D8-A1JP-01 TCGA-D8-A1JS-01 TCGA-D8-A1JT-01 TCGA-D8-A1JU-01 TCGA-D8-A1X5-01 TCGA-D8-A1X6-01 TCGA-D8-A1X7-01 TCGA-D8-A1X8-01 TCGA-D8-A1X9-01 TCGA-D8-A1XA-01 TCGA-D8-A1XB-01 TCGA-D8-A1XC-01 TCGA-D8-A1XD-01 TCGA-D8-A1XF-01 TCGA-D8-A1XG-01 TCGA-D8-A1XJ-01 TCGA-D8-A1XK-01 TCGA-D8-A1XL-01 TCGA-D8-A1XM-01 TCGA-D8-A1XO-01 TCGA-D8-A1XQ-01 TCGA-D8-A1XR-01 TCGA-D8-A1XS-01 TCGA-D8-A1XT-01 TCGA-D8-A1XU-01 TCGA-D8-A1XV-01 TCGA-D8-A1XW-01 TCGA-D8-A1XY-01 TCGA-D8-A1XZ-01 TCGA-D8-A1Y0-01 TCGA-D8-A1Y1-01 TCGA-D8-A1Y2-01 TCGA-D8-A1Y3-01 TCGA-D8-A27E-01 TCGA-D8-A27F-01 TCGA-D8-A27G-01 TCGA-D8-A27H-01 TCGA-D8-A27I-01 TCGA-D8-A27K-01 TCGA-D8-A27L-01 TCGA-D8-A27M-01 TCGA-D8-A27N-01 TCGA-D8-A27P-01 TCGA-D8-A27R-01 TCGA-D8-A27T-01 TCGA-D8-A27V-01 TCGA-D8-A27W-01 TCGA-D8-A3Z5-01 TCGA-D8-A3Z6-01 TCGA-D8-A4Z1-01 TCGA-D8-A73U-01 TCGA-D8-A73W-01 TCGA-D8-A73X-01 TCGA-E2-A105-01 TCGA-E2-A107-01 TCGA-E2-A108-01 TCGA-E2-A109-01 TCGA-E2-A10B-01 TCGA-E2-A10C-01 TCGA-E2-A10E-01 TCGA-E2-A10F-01 TCGA-E2-A14N-01 TCGA-E2-A14U-01 TCGA-E2-A15I-01 TCGA-E2-A15J-01 TCGA-E2-A15K-01 TCGA-E2-A1AZ-01 TCGA-E2-A1B0-01 TCGA-E2-A1B1-01 TCGA-E2-A1B4-01 TCGA-E2-A1B5-01 TCGA-E2-A1B6-01 TCGA-E2-A1BC-01 TCGA-E2-A1BD-01 TCGA-E2-A1IE-01 TCGA-E2-A1IF-01 TCGA-E2-A1IG-01 TCGA-E2-A1IH-01 TCGA-E2-A1II-01 TCGA-E2-A1IJ-01 TCGA-E2-A1IK-01 TCGA-E2-A1IL-01 TCGA-E2-A1IN-01 TCGA-E2-A1IO-01 TCGA-E2-A1IU-01 TCGA-E2-A1L6-01 TCGA-E2-A1L7-01 TCGA-E2-A1L8-01 TCGA-E2-A1L9-01 TCGA-E2-A1LA-01 TCGA-E2-A1LB-01 TCGA-E2-A1LE-01 TCGA-E2-A1LG-01 TCGA-E2-A1LH-01 TCGA-E2-A1LI-01 TCGA-E2-A1LK-01 TCGA-E2-A1LL-01 TCGA-E2-A1LS-01 TCGA-E2-A2P5-01 TCGA-E2-A2P6-01 TCGA-E2-A3DX-01 TCGA-E2-A56Z-01 TCGA-E2-A570-01 TCGA-E2-A573-01 TCGA-E2-A574-01 TCGA-E2-A576-01 TCGA-E2-A9RU-01 TCGA-E9-A1N3-01 TCGA-E9-A1N4-01 TCGA-E9-A1N5-01 TCGA-E9-A1N6-01 TCGA-E9-A1N8-01 TCGA-E9-A1N9-01 TCGA-E9-A1NA-01 TCGA-E9-A1NC-01 TCGA-E9-A1ND-01 TCGA-E9-A1NE-01 TCGA-E9-A1NF-01 TCGA-E9-A1NG-01 TCGA-E9-A1NH-01 TCGA-E9-A1NI-01 TCGA-E9-A1QZ-01 TCGA-E9-A1R0-01 TCGA-E9-A1R2-01 TCGA-E9-A1R3-01 TCGA-E9-A1R4-01 TCGA-E9-A1R5-01 TCGA-E9-A1R6-01 TCGA-E9-A1R7-01 TCGA-E9-A1RA-01 TCGA-E9-A1RB-01 TCGA-E9-A1RC-01 TCGA-E9-A1RD-01 TCGA-E9-A1RE-01 TCGA-E9-A1RF-01 TCGA-E9-A1RG-01 TCGA-E9-A1RH-01 TCGA-E9-A1RI-01 TCGA-E9-A226-01 TCGA-E9-A227-01 TCGA-E9-A228-01 TCGA-E9-A229-01 TCGA-E9-A22A-01 TCGA-E9-A22B-01 TCGA-E9-A22D-01 TCGA-E9-A22E-01 TCGA-E9-A22G-01 TCGA-E9-A22H-01 TCGA-E9-A243-01 TCGA-E9-A244-01 TCGA-E9-A245-01 TCGA-E9-A247-01 TCGA-E9-A248-01 TCGA-E9-A249-01 TCGA-E9-A24A-01 TCGA-E9-A295-01 TCGA-E9-A2JS-01 TCGA-E9-A2JT-01 TCGA-E9-A3HO-01 TCGA-E9-A3Q9-01 TCGA-E9-A3QA-01 TCGA-E9-A3X8-01 TCGA-E9-A54X-01 TCGA-E9-A54Y-01 TCGA-E9-A5FK-01 TCGA-E9-A5FL-01 TCGA-E9-A5UO-01 TCGA-E9-A5UP-01 TCGA-E9-A6HE-01 TCGA-EW-A1IW-01 TCGA-EW-A1IX-01 TCGA-EW-A1IY-01 TCGA-EW-A1IZ-01 TCGA-EW-A1J1-01 TCGA-EW-A1J2-01 TCGA-EW-A1J3-01 TCGA-EW-A1J5-01 TCGA-EW-A1J6-01 TCGA-EW-A1OV-01 TCGA-EW-A1OW-01 TCGA-EW-A1OX-01 TCGA-EW-A1OY-01 TCGA-EW-A1OZ-01 TCGA-EW-A1P0-01 TCGA-EW-A1P1-01 TCGA-EW-A1P3-01 TCGA-EW-A1P4-01 TCGA-EW-A1P5-01 TCGA-EW-A1P6-01 TCGA-EW-A1P7-01 TCGA-EW-A1P8-01 TCGA-EW-A1PA-01 TCGA-EW-A1PB-01 TCGA-EW-A1PC-01 TCGA-EW-A1PD-01 TCGA-EW-A1PE-01 TCGA-EW-A1PF-01 TCGA-EW-A1PG-01 TCGA-EW-A1PH-01 TCGA-EW-A2FR-01 TCGA-EW-A2FS-01 TCGA-EW-A2FV-01 TCGA-EW-A2FW-01 TCGA-EW-A3E8-01 TCGA-EW-A3U0-01 TCGA-EW-A423-01 TCGA-EW-A424-01 TCGA-EW-A6S9-01 TCGA-EW-A6SA-01 TCGA-EW-A6SB-01 TCGA-EW-A6SC-01 TCGA-EW-A6SD-01 TCGA-GI-A2C8-01 TCGA-GI-A2C9-01 TCGA-GM-A2D9-01 TCGA-GM-A2DA-01 TCGA-GM-A2DB-01 TCGA-GM-A2DC-01 TCGA-GM-A2DD-01 TCGA-GM-A2DF-01 TCGA-GM-A2DH-01 TCGA-GM-A2DI-01 TCGA-GM-A2DK-01 TCGA-GM-A2DL-01 TCGA-GM-A2DM-01 TCGA-GM-A2DN-01 TCGA-GM-A2DO-01 TCGA-GM-A3NW-01 TCGA-GM-A3NY-01 TCGA-GM-A3XG-01 TCGA-GM-A3XL-01 TCGA-GM-A3XN-01 TCGA-GM-A4E0-01 TCGA-GM-A5PV-01 TCGA-GM-A5PX-01 TCGA-HN-A2NL-01 TCGA-HN-A2OB-01 TCGA-JL-A3YW-01 TCGA-JL-A3YX-01 TCGA-LD-A66U-01 TCGA-LD-A74U-01 TCGA-LD-A7W5-01 TCGA-LD-A7W6-01 TCGA-LD-A9QF-01 TCGA-LL-A440-01 TCGA-LL-A441-01 TCGA-LL-A442-01 TCGA-LL-A50Y-01 TCGA-LL-A5YL-01 TCGA-LL-A5YM-01 TCGA-LL-A5YN-01 TCGA-LL-A5YO-01 TCGA-LL-A5YP-01 TCGA-LL-A6FP-01 TCGA-LL-A6FQ-01 TCGA-LL-A6FR-01 TCGA-LL-A73Y-01 TCGA-LL-A73Z-01 TCGA-LL-A740-01 TCGA-LL-A7SZ-01 TCGA-LL-A7T0-01 TCGA-LL-A8F5-01 TCGA-LL-A9Q3-01 TCGA-LQ-A4E4-01 TCGA-MS-A51U-01 TCGA-OK-A5Q2-01 TCGA-OL-A5D6-01 TCGA-OL-A5D7-01 TCGA-OL-A5D8-01 TCGA-OL-A5DA-01 TCGA-OL-A5RU-01 TCGA-OL-A5RV-01 TCGA-OL-A5RW-01 TCGA-OL-A5RX-01 TCGA-OL-A5RY-01 TCGA-OL-A5RZ-01 TCGA-OL-A5S0-01 TCGA-OL-A66H-01 TCGA-OL-A66I-01 TCGA-OL-A66J-01 TCGA-OL-A66K-01 TCGA-OL-A66L-01 TCGA-OL-A66N-01 TCGA-OL-A66O-01 TCGA-OL-A66P-01 TCGA-OL-A6VO-01 TCGA-OL-A6VQ-01 TCGA-OL-A6VR-01 TCGA-OL-A97C-01 TCGA-PE-A5DC-01 TCGA-PE-A5DD-01 TCGA-PE-A5DE-01 TCGA-PL-A8LV-01 TCGA-PL-A8LX-01 TCGA-PL-A8LY-01 TCGA-PL-A8LZ-01 TCGA-S3-A6ZF-01 TCGA-S3-A6ZG-01 TCGA-S3-A6ZH-01 TCGA-S3-AA0Z-01 TCGA-S3-AA10-01 TCGA-S3-AA11-01 TCGA-S3-AA12-01 TCGA-S3-AA14-01 TCGA-S3-AA15-01 TCGA-S3-AA17-01 TCGA-UL-AAZ6-01 TCGA-UU-A93S-01 TCGA-V7-A7HQ-01 TCGA-W8-A86G-01 TCGA-WT-AB41-01 TCGA-WT-AB44-01 TCGA-XX-A899-01 TCGA-XX-A89A-01 TCGA-Z7-A8R5-01 TCGA-Z7-A8R6-01
|
initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_phosphoprotein_quantification.txt
ADDED
|
@@ -0,0 +1,6 @@
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|
|
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|
|
|
|
| 1 |
+
cancer_study_identifier: brca_tcga_pan_can_atlas_2018
|
| 2 |
+
stable_id: brca_tcga_pan_can_atlas_2018_phosphoprotein_quantification
|
| 3 |
+
case_list_name: Samples with phosphoprotein quantification data (mass spectrometry by CPTAC)
|
| 4 |
+
case_list_description: Tumor samples with phosphoprotein quantification data (105 samples)
|
| 5 |
+
case_list_category: other
|
| 6 |
+
case_list_ids: TCGA-A2-A0D0-01 TCGA-BH-A0HK-01 TCGA-C8-A12T-01 TCGA-A2-A0D2-01 TCGA-C8-A12U-01 TCGA-AR-A1AS-01 TCGA-A2-A0EV-01 TCGA-AN-A0AM-01 TCGA-D8-A142-01 TCGA-A2-A0SW-01 TCGA-AO-A0JL-01 TCGA-BH-A0BV-01 TCGA-A2-A0T6-01 TCGA-E2-A158-01 TCGA-E2-A15A-01 TCGA-A2-A0T7-01 TCGA-C8-A12Q-01 TCGA-A8-A079-01 TCGA-A2-A0YF-01 TCGA-BH-A0DD-01 TCGA-BH-A0E9-01 TCGA-A2-A0YG-01 TCGA-E2-A150-01 TCGA-BH-A18N-01 TCGA-A2-A0YM-01 TCGA-BH-A0C7-01 TCGA-A2-A0SX-01 TCGA-A7-A0CD-01 TCGA-C8-A12W-01 TCGA-AN-A0AL-01 TCGA-A7-A0CE-01 TCGA-BH-A0C0-01 TCGA-A2-A0YC-01 TCGA-A7-A0CJ-01 TCGA-AO-A12F-01 TCGA-A2-A0YL-01 TCGA-A8-A06Z-01 TCGA-A2-A0D1-01 TCGA-A2-A0CM-01 TCGA-A8-A09G-01 TCGA-C8-A131-01 TCGA-C8-A134-01 TCGA-A8-A09I-01 TCGA-C8-A12L-01 TCGA-A2-A0EX-01 TCGA-AN-A0FL-01 TCGA-BH-A0DG-01 TCGA-AN-A0AS-01 TCGA-AO-A0JC-01 TCGA-A8-A08Z-01 TCGA-AR-A0TX-01 TCGA-AO-A0JE-01 TCGA-A2-A0T2-01 TCGA-AN-A0AJ-01 TCGA-AO-A0JM-01 TCGA-C8-A12V-01 TCGA-A8-A08G-01 TCGA-AO-A12D-01 TCGA-AN-A04A-01 TCGA-BH-A0AV-01 TCGA-AO-A12B-01 TCGA-AO-A12E-01 TCGA-A8-A06N-01 TCGA-A2-A0T1-01 TCGA-AR-A0TR-01 TCGA-AO-A03O-01 TCGA-BH-A18R-01 TCGA-AR-A0TT-01 TCGA-AR-A1AQ-01 TCGA-AR-A0TV-01 TCGA-C8-A12Z-01 TCGA-AO-A0JJ-01 TCGA-AR-A0TY-01 TCGA-AR-A0U4-01 TCGA-BH-A0HP-01 TCGA-AR-A1AP-01 TCGA-AN-A0FK-01 TCGA-AO-A0J6-01 TCGA-AR-A1AW-01 TCGA-AR-A1AV-01 TCGA-C8-A135-01 TCGA-BH-A0EE-01 TCGA-AO-A0J9-01 TCGA-BH-A0E0-01 TCGA-BH-A18U-01 TCGA-A2-A0YI-01 TCGA-A2-A0EQ-01 TCGA-BH-A18V-01 TCGA-A7-A13F-01 TCGA-BH-A0E1-01 TCGA-C8-A12P-01 TCGA-BH-A0C1-01 TCGA-A2-A0EY-01 TCGA-C8-A138-01 TCGA-E2-A154-01 TCGA-BH-A0BZ-01 TCGA-D8-A13Y-01 TCGA-A8-A076-01 TCGA-AO-A126-01 TCGA-E2-A10A-01 TCGA-BH-A18Q-01 TCGA-C8-A130-01 TCGA-E2-A159-01 TCGA-A2-A0T3-01 TCGA-A2-A0YD-01
|
initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_protein_quantification.txt
ADDED
|
@@ -0,0 +1,6 @@
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|
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|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
cancer_study_identifier: brca_tcga_pan_can_atlas_2018
|
| 2 |
+
stable_id: brca_tcga_pan_can_atlas_2018_protein_quantification
|
| 3 |
+
case_list_name: Samples with protein data (Mass Spec)
|
| 4 |
+
case_list_description: Samples with protein data (Mass Spec) (105 samples)
|
| 5 |
+
case_list_category: other
|
| 6 |
+
case_list_ids: TCGA-A2-A0T3-01 TCGA-A2-A0YL-01 TCGA-AO-A126-01 TCGA-A2-A0YI-01 TCGA-AO-A0J6-01 TCGA-AR-A1AP-01 TCGA-A8-A08G-01 TCGA-A2-A0YD-01 TCGA-C8-A134-01 TCGA-E2-A150-01 TCGA-BH-A0E9-01 TCGA-A8-A06N-01 TCGA-A2-A0D1-01 TCGA-A7-A0CE-01 TCGA-A2-A0YM-01 TCGA-A2-A0YC-01 TCGA-AO-A03O-01 TCGA-D8-A142-01 TCGA-A8-A079-01 TCGA-A2-A0T1-01 TCGA-A7-A0CJ-01 TCGA-A2-A0D0-01 TCGA-AR-A0TT-01 TCGA-C8-A130-01 TCGA-BH-A18R-01 TCGA-A2-A0YF-01 TCGA-A2-A0CM-01 TCGA-BH-A0EE-01 TCGA-A2-A0T6-01 TCGA-AR-A0TX-01 TCGA-A2-A0T2-01 TCGA-AO-A12E-01 TCGA-E2-A10A-01 TCGA-A2-A0D2-01 TCGA-AO-A0JC-01 TCGA-A8-A08Z-01 TCGA-D8-A13Y-01 TCGA-BH-A0AV-01 TCGA-E2-A159-01 TCGA-A2-A0EY-01 TCGA-A2-A0EX-01 TCGA-A7-A0CD-01 TCGA-A2-A0EV-01 TCGA-AR-A0TY-01 TCGA-A2-A0SX-01 TCGA-A2-A0SW-01 TCGA-A7-A13F-01 TCGA-BH-A18N-01 TCGA-BH-A0E1-01 TCGA-C8-A135-01 TCGA-AN-A04A-01 TCGA-BH-A0DD-01 TCGA-A2-A0EQ-01 TCGA-C8-A12T-01 TCGA-AN-A0FL-01 TCGA-C8-A138-01 TCGA-E2-A158-01 TCGA-C8-A12Q-01 TCGA-AR-A0TV-01 TCGA-AN-A0AL-01 TCGA-A8-A06Z-01 TCGA-A8-A076-01 TCGA-AR-A0TR-01 TCGA-E2-A15A-01 TCGA-AN-A0AS-01 TCGA-BH-A0E0-01 TCGA-AO-A0JM-01 TCGA-E2-A154-01 TCGA-AO-A0J9-01 TCGA-C8-A12U-01 TCGA-BH-A18V-01 TCGA-BH-A18U-01 TCGA-AO-A0JJ-01 TCGA-BH-A0C0-01 TCGA-AR-A1AQ-01 TCGA-BH-A18Q-01 TCGA-A8-A09I-01 TCGA-AO-A12B-01 TCGA-C8-A131-01 TCGA-BH-A0DG-01 TCGA-C8-A12P-01 TCGA-BH-A0BV-01 TCGA-BH-A0C7-01 TCGA-AO-A0JL-01 TCGA-BH-A0HP-01 TCGA-C8-A12Z-01 TCGA-BH-A0C1-01 TCGA-A2-A0YG-01 TCGA-AR-A0U4-01 TCGA-AR-A1AV-01 TCGA-C8-A12W-01 TCGA-A8-A09G-01 TCGA-AN-A0AM-01 TCGA-AO-A12F-01 TCGA-AN-A0AJ-01 TCGA-AO-A12D-01 TCGA-AR-A1AS-01 TCGA-AO-A0JE-01 TCGA-BH-A0HK-01 TCGA-AN-A0FK-01 TCGA-C8-A12L-01 TCGA-A2-A0T7-01 TCGA-BH-A0BZ-01 TCGA-AR-A1AW-01 TCGA-C8-A12V-01
|
initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_rppa.txt
ADDED
|
@@ -0,0 +1,6 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
cancer_study_identifier: brca_tcga_pan_can_atlas_2018
|
| 2 |
+
stable_id: brca_tcga_pan_can_atlas_2018_rppa
|
| 3 |
+
case_list_name: Samples with protein data (RPPA)
|
| 4 |
+
case_list_description: Samples with protein data (RPPA) (876 samples)
|
| 5 |
+
case_list_category: all_cases_with_rppa_data
|
| 6 |
+
case_list_ids: TCGA-3C-AALK-01 TCGA-AR-A1AH-01 TCGA-EW-A2FW-01 TCGA-E9-A1R0-01 TCGA-AR-A1AJ-01 TCGA-E9-A1QZ-01 TCGA-E9-A1R2-01 TCGA-GM-A2DK-01 TCGA-AR-A255-01 TCGA-E2-A10B-01 TCGA-C8-A1HL-01 TCGA-EW-A2FS-01 TCGA-D8-A1XA-01 TCGA-AO-A1KQ-01 TCGA-A7-A3RF-01 TCGA-GM-A2D9-01 TCGA-D8-A3Z5-01 TCGA-AR-A1AT-01 TCGA-EW-A1P5-01 TCGA-B6-A0RO-01 TCGA-E9-A1NA-01 TCGA-LD-A66U-01 TCGA-BH-A1EN-01 TCGA-BH-A0W4-01 TCGA-EW-A1PD-01 TCGA-E9-A1N5-01 TCGA-D8-A1J8-01 TCGA-B6-A0RV-01 TCGA-E2-A15R-01 TCGA-E9-A3QA-01 TCGA-S3-AA15-01 TCGA-A7-A0CE-01 TCGA-A7-A0CG-01 TCGA-A2-A3XX-01 TCGA-BH-A0EB-01 TCGA-AN-A0XP-01 TCGA-E9-A3X8-01 TCGA-GM-A2DC-01 TCGA-AR-A24N-01 TCGA-D8-A27T-01 TCGA-E2-A1B0-01 TCGA-BH-A1EY-01 TCGA-EW-A6S9-01 TCGA-A2-A0CQ-01 TCGA-GM-A2DN-01 TCGA-E2-A152-01 TCGA-AO-A03M-01 TCGA-A2-A3XT-01 TCGA-A7-A4SE-01 TCGA-BH-A0DT-01 TCGA-Z7-A8R5-01 TCGA-A1-A0SJ-01 TCGA-AR-A2LJ-01 TCGA-AQ-A1H3-01 TCGA-D8-A1JB-01 TCGA-B6-A0IQ-01 TCGA-BH-A0BC-01 TCGA-S3-AA17-01 TCGA-BH-A1FG-01 TCGA-AR-A0TS-01 TCGA-AN-A0G0-01 TCGA-BH-A18R-01 TCGA-D8-A27P-01 TCGA-D8-A1JD-01 TCGA-E2-A1IL-01 TCGA-A7-A3IZ-01 TCGA-A2-A0CM-01 TCGA-OL-A66J-01 TCGA-AR-A2LO-01 TCGA-A8-A08L-01 TCGA-BH-A201-01 TCGA-LL-A5YM-01 TCGA-BH-A0BO-01 TCGA-A2-A0T2-01 TCGA-A8-A06X-01 TCGA-D8-A143-01 TCGA-AR-A0TP-01 TCGA-C8-A134-01 TCGA-A2-A0D2-01 TCGA-EW-A1P0-01 TCGA-A2-A4RW-01 TCGA-A2-A1G0-01 TCGA-D8-A1XV-01 TCGA-A8-A09B-01 TCGA-D8-A13Y-01 TCGA-AR-A0TU-01 TCGA-A2-A0EP-01 TCGA-C8-A12Y-01 TCGA-A2-A0YT-01 TCGA-A8-A07I-01 TCGA-D8-A1JI-01 TCGA-E2-A15P-01 TCGA-A8-A099-01 TCGA-OL-A5RX-01 TCGA-BH-A0HN-01 TCGA-E9-A1R6-01 TCGA-A2-A0EY-01 TCGA-D8-A1XZ-01 TCGA-E9-A1ND-01 TCGA-LL-A6FQ-01 TCGA-EW-A1OY-01 TCGA-B6-A0RP-01 TCGA-BH-A1FD-01 TCGA-LL-A9Q3-01 TCGA-GM-A2DL-01 TCGA-E9-A248-01 TCGA-A2-A0SW-01 TCGA-E2-A1B6-01 TCGA-PE-A5DE-01 TCGA-BH-A18N-01 TCGA-E9-A1RD-01 TCGA-E2-A14Q-01 TCGA-AC-A2BM-01 TCGA-BH-A42T-01 TCGA-BH-A0B1-01 TCGA-E2-A15K-01 TCGA-BH-A0EA-01 TCGA-A2-A1FZ-01 TCGA-A2-A0CZ-01 TCGA-C8-A12Q-01 TCGA-D8-A27W-01 TCGA-BH-A0BA-01 TCGA-B6-A0RT-01 TCGA-AR-A1AY-01 TCGA-A2-A25C-01 TCGA-AN-A0XS-01 TCGA-OL-A5DA-01 TCGA-D8-A27R-01 TCGA-E2-A15A-01 TCGA-A7-A5ZV-01 TCGA-LL-A50Y-01 TCGA-B6-A0WX-01 TCGA-AO-A0J8-01 TCGA-C8-A26Z-01 TCGA-A2-A04Q-01 TCGA-E2-A14Y-01 TCGA-BH-A1FN-01 TCGA-BH-A0E0-01 TCGA-E9-A2JT-01 TCGA-AO-A0J7-01 TCGA-E2-A15G-01 TCGA-AO-A0J9-01 TCGA-C8-A12U-01 TCGA-AO-A03P-01 TCGA-A8-A09R-01 TCGA-E2-A107-01 TCGA-E9-A3HO-01 TCGA-A8-A091-01 TCGA-D8-A1XT-01 TCGA-AR-A1AQ-01 TCGA-MS-A51U-01 TCGA-AC-A6IX-01 TCGA-D8-A1Y2-01 TCGA-PL-A8LY-01 TCGA-BH-A0BP-01 TCGA-C8-A131-01 TCGA-D8-A1XJ-01 TCGA-BH-A0DG-01 TCGA-C8-A3M7-01 TCGA-AN-A0AR-01 TCGA-E2-A1L6-01 TCGA-A2-A0EO-01 TCGA-BH-A0BV-01 TCGA-EW-A6SC-01 TCGA-E2-A109-01 TCGA-B6-A0I2-01 TCGA-AR-A1AM-01 TCGA-4H-AAAK-01 TCGA-AC-A5XS-01 TCGA-AC-A5EI-01 TCGA-E2-A14S-01 TCGA-XX-A899-01 TCGA-BH-A209-01 TCGA-AO-A03U-01 TCGA-A2-A3KD-01 TCGA-D8-A1JM-01 TCGA-BH-A1FL-01 TCGA-A2-A04W-01 TCGA-AN-A041-01 TCGA-E9-A1NI-01 TCGA-LL-A6FP-01 TCGA-E9-A226-01 TCGA-C8-A12Z-01 TCGA-E2-A1AZ-01 TCGA-D8-A1X8-01 TCGA-A2-A0T5-01 TCGA-BH-A0EI-01 TCGA-AO-A0JG-01 TCGA-LD-A74U-01 TCGA-E9-A1NF-01 TCGA-C8-A1HM-01 TCGA-AC-A62X-01 TCGA-S3-AA11-01 TCGA-A8-A07R-01 TCGA-AN-A0FK-01 TCGA-E9-A1RA-01 TCGA-BH-A0HA-01 TCGA-A2-A0T7-01 TCGA-A2-A0D4-01 TCGA-E9-A22G-01 TCGA-LL-A740-01 TCGA-A2-A0CV-01 TCGA-BH-A0C1-01 TCGA-AC-A2QI-01 TCGA-D8-A27M-01 TCGA-A8-A081-01 TCGA-BH-A0BZ-01 TCGA-BH-A0RX-01 TCGA-S3-A6ZG-01 TCGA-E9-A1NG-01 TCGA-A2-A0YC-01 TCGA-EW-A2FV-01 TCGA-AO-A0J5-01 TCGA-A8-A08T-01 TCGA-BH-A1FJ-01 TCGA-BH-A0DV-01 TCGA-A8-A07Z-01 TCGA-A8-A08P-01 TCGA-A2-A0YI-01 TCGA-AC-A2QJ-01 TCGA-EW-A1PE-01 TCGA-BH-A0H6-01 TCGA-BH-A0BM-01 TCGA-A7-A2KD-01 TCGA-A8-A06P-01 TCGA-D8-A27I-01 TCGA-S3-AA14-01 TCGA-A8-A08H-01 TCGA-BH-A0BF-01 TCGA-HN-A2NL-01 TCGA-JL-A3YW-01 TCGA-E2-A14V-01 TCGA-AN-A0XN-01 TCGA-BH-A0E9-01 TCGA-A1-A0SK-01 TCGA-E9-A6HE-01 TCGA-AO-A12A-01 TCGA-BH-A1EX-01 TCGA-LL-A441-01 TCGA-A2-A04U-01 TCGA-E9-A247-01 TCGA-A2-A0YM-01 TCGA-BH-A0DP-01 TCGA-GM-A2DF-01 TCGA-AR-A2LN-01 TCGA-D8-A1JF-01 TCGA-OL-A6VQ-01 TCGA-AR-A252-01 TCGA-AO-A129-01 TCGA-A2-A25F-01 TCGA-PE-A5DC-01 TCGA-D8-A142-01 TCGA-GM-A2DO-01 TCGA-E2-A1LL-01 TCGA-C8-A273-01 TCGA-LD-A9QF-01 TCGA-E2-A153-01 TCGA-E2-A15L-01 TCGA-BH-A0AU-01 TCGA-A2-A0T1-01 TCGA-A7-A0CJ-01 TCGA-A2-A0CS-01 TCGA-AR-A24W-01 TCGA-EW-A1P1-01 TCGA-E2-A9RU-01 TCGA-AR-A0TT-01 TCGA-C8-A132-01 TCGA-AC-A3W6-01 TCGA-D8-A1JJ-01 TCGA-C8-A130-01 TCGA-E2-A1B4-01 TCGA-A8-A0A4-01 TCGA-D8-A1JH-01 TCGA-E9-A5UP-01 TCGA-A2-A1G4-01 TCGA-AR-A24L-01 TCGA-A2-A0D3-01 TCGA-BH-A1ET-01 TCGA-AO-A12G-01 TCGA-C8-A1HI-01 TCGA-AR-A0TX-01 TCGA-C8-A1HO-01 TCGA-OL-A66N-01 TCGA-A2-A1FV-01 TCGA-D8-A1XC-01 TCGA-A7-A4SC-01 TCGA-AC-A2FM-01 TCGA-AR-A2LH-01 TCGA-LL-A6FR-01 TCGA-B6-A0RU-01 TCGA-GM-A2DB-01 TCGA-LL-A5YO-01 TCGA-E9-A1N3-01 TCGA-A8-A08Z-01 TCGA-PL-A8LV-01 TCGA-E2-A15H-01 TCGA-A8-A08O-01 TCGA-C8-A1HF-01 TCGA-E2-A15J-01 TCGA-E9-A244-01 TCGA-E9-A24A-01 TCGA-BH-A0B0-01 TCGA-BH-A1FR-01 TCGA-A1-A0SQ-01 TCGA-AN-A0FW-01 TCGA-A2-A0SV-01 TCGA-BH-A1FC-01 TCGA-E9-A22B-01 TCGA-A2-A3XV-01 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TCGA-A2-A0EU-01 TCGA-BH-A1FE-01 TCGA-BH-A0H7-01 TCGA-A8-A09C-01 TCGA-A2-A0CL-01 TCGA-BH-A18L-01 TCGA-AC-A6IW-01 TCGA-A2-A0EX-01 TCGA-EW-A1J5-01 TCGA-WT-AB41-01 TCGA-LL-A5YL-01 TCGA-D8-A1XR-01 TCGA-AO-A0JB-01 TCGA-C8-A274-01 TCGA-C8-A27A-01 TCGA-AR-A1AK-01 TCGA-AR-A0TQ-01 TCGA-AN-A0AT-01 TCGA-C8-A26X-01 TCGA-C8-A135-01 TCGA-E9-A22A-01 TCGA-A7-A3J1-01 TCGA-BH-A18M-01 TCGA-D8-A1Y3-01 TCGA-AC-A3YJ-01 TCGA-E9-A22E-01 TCGA-A2-A0EQ-01 TCGA-D8-A1XW-01 TCGA-D8-A1Y1-01 TCGA-BH-A0DK-01 TCGA-AN-A0FL-01 TCGA-C8-A12O-01 TCGA-EW-A2FR-01 TCGA-BH-A18P-01 TCGA-BH-A0BT-01 TCGA-AC-A2FE-01 TCGA-AO-A03N-01 TCGA-LL-A5YP-01 TCGA-BH-A0E2-01 TCGA-A8-A076-01 TCGA-BH-A203-01 TCGA-AR-A0U4-01 TCGA-E2-A1B5-01 TCGA-A8-A06U-01 TCGA-A2-A0YD-01 TCGA-E9-A1R7-01 TCGA-OL-A66P-01 TCGA-E9-A249-01 TCGA-LL-A442-01 TCGA-AC-A2BK-01 TCGA-E2-A1BD-01 TCGA-AC-A23C-01 TCGA-LD-A7W6-01 TCGA-A2-A04N-01 TCGA-C8-A1HE-01 TCGA-D8-A1XM-01 TCGA-C8-A1HG-01 TCGA-D8-A1XS-01 TCGA-E9-A227-01 TCGA-AN-A0AK-01 TCGA-BH-A1EU-01 TCGA-OL-A5D7-01 TCGA-A8-A07P-01 TCGA-GM-A2DD-01 TCGA-E9-A245-01 TCGA-OL-A6VO-01 TCGA-S3-AA0Z-01 TCGA-AC-A23E-01 TCGA-BH-A0B3-01 TCGA-D8-A1JS-01 TCGA-B6-A0X0-01 TCGA-EW-A424-01 TCGA-AO-A1KS-01 TCGA-AC-A4ZE-01 TCGA-A2-A0CW-01 TCGA-A7-A425-01 TCGA-B6-A0IK-01 TCGA-A2-A0CU-01 TCGA-AR-A24U-01 TCGA-E9-A1RF-01 TCGA-AN-A0FD-01 TCGA-BH-A18G-01 TCGA-LL-A73Z-01 TCGA-E2-A15E-01 TCGA-B6-A0I8-01 TCGA-E2-A1L7-01 TCGA-5T-A9QA-01 TCGA-AO-A0J6-01 TCGA-AR-A24S-01 TCGA-BH-A8FZ-01 TCGA-A2-A0YG-01 TCGA-AC-A2FG-01 TCGA-AO-A0J2-01 TCGA-AR-A1AL-01 TCGA-EW-A1IZ-01 TCGA-C8-A12W-01 TCGA-BH-A1EO-01 TCGA-A8-A09G-01 TCGA-D8-A13Z-01 TCGA-C8-A12L-01 TCGA-BH-A28Q-01 TCGA-LL-A7SZ-01 TCGA-EW-A1J1-01 TCGA-AN-A0AM-01 TCGA-D8-A1XK-01 TCGA-A7-A4SA-01 TCGA-A8-A09W-01 TCGA-A2-A4S0-01 TCGA-A7-A26H-01 TCGA-AC-A2FB-01 TCGA-AC-A8OQ-01 TCGA-E2-A3DX-01 TCGA-EW-A1PB-01 TCGA-D8-A1JU-01 TCGA-A7-A6VX-01 TCGA-D8-A147-01 TCGA-B6-A0RQ-01 TCGA-A2-A0YK-01 TCGA-E9-A1N8-01 TCGA-A7-A26I-01 TCGA-A8-A085-01 TCGA-AN-A0FZ-01 TCGA-E2-A574-01 TCGA-A1-A0SO-01 TCGA-BH-A0DI-01 TCGA-E2-A1IG-01 TCGA-AR-A0U0-01 TCGA-E9-A1NH-01 TCGA-EW-A6SA-01 TCGA-AR-A24Q-01 TCGA-BH-A1F0-01 TCGA-GM-A4E0-01 TCGA-AC-A5XU-01
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initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_sequenced.txt
ADDED
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@@ -0,0 +1,6 @@
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+
cancer_study_identifier: brca_tcga_pan_can_atlas_2018
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| 2 |
+
stable_id: brca_tcga_pan_can_atlas_2018_sequenced
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| 3 |
+
case_list_name: Samples with mutation data
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| 4 |
+
case_list_description: Samples with mutation data (1066 samples)
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| 5 |
+
case_list_category: all_cases_with_mutation_data
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| 6 |
+
case_list_ids: TCGA-OL-A66H-01 TCGA-3C-AALK-01 TCGA-AR-A1AH-01 TCGA-AR-A1AJ-01 TCGA-AC-A62Y-01 TCGA-E9-A1QZ-01 TCGA-E2-A10B-01 TCGA-C8-A1HL-01 TCGA-EW-A2FS-01 TCGA-D8-A1XA-01 TCGA-AO-A1KQ-01 TCGA-A8-A0A6-01 TCGA-B6-A0IE-01 TCGA-GM-A2D9-01 TCGA-AQ-A04J-01 TCGA-E9-A1RD-01 TCGA-LD-A66U-01 TCGA-BH-A1EN-01 TCGA-BH-A1FN-01 TCGA-E2-A15R-01 TCGA-E9-A3QA-01 TCGA-BH-A0H0-01 TCGA-A2-A3XX-01 TCGA-BH-A0EB-01 TCGA-GM-A2DK-01 TCGA-BH-A1EY-01 TCGA-AC-A8OS-01 TCGA-BH-A18K-01 TCGA-A7-A4SE-01 TCGA-BH-A0DT-01 TCGA-AC-A6IV-01 TCGA-LL-A7SZ-01 TCGA-A1-A0SJ-01 TCGA-AR-A2LJ-01 TCGA-D8-A1X5-01 TCGA-D8-A1JB-01 TCGA-BH-A0BC-01 TCGA-AN-A0G0-01 TCGA-AO-A03T-01 TCGA-D8-A27P-01 TCGA-D8-A1JD-01 TCGA-E2-A570-01 TCGA-OL-A66J-01 TCGA-AR-A2LO-01 TCGA-E9-A5FL-01 TCGA-BH-A201-01 TCGA-LL-A5YM-01 TCGA-A2-A0T2-01 TCGA-AR-A0TP-01 TCGA-EW-A1P0-01 TCGA-A2-A4RW-01 TCGA-D8-A1XV-01 TCGA-A7-A3RF-01 TCGA-D8-A13Y-01 TCGA-AR-A0TU-01 TCGA-A8-A07L-01 TCGA-A8-A07I-01 TCGA-D8-A1JI-01 TCGA-E2-A15P-01 TCGA-OL-A5RX-01 TCGA-A2-A0EY-01 TCGA-BH-A0B8-01 TCGA-XX-A89A-01 TCGA-EW-A1OY-01 TCGA-B6-A0RP-01 TCGA-LL-A9Q3-01 TCGA-A1-A0SQ-01 TCGA-AR-A5QM-01 TCGA-D8-A27V-01 TCGA-EW-A1P5-01 TCGA-BH-A18N-01 TCGA-AC-A23H-01 TCGA-BH-A0B1-01 TCGA-AN-A0FW-01 TCGA-A2-A1FZ-01 TCGA-A2-A0SV-01 TCGA-BH-A0BA-01 TCGA-E2-A2P6-01 TCGA-B6-A0RT-01 TCGA-D8-A27R-01 TCGA-C8-A26Z-01 TCGA-BH-A1FU-01 TCGA-E2-A14Y-01 TCGA-AO-A1KO-01 TCGA-OL-A5D6-01 TCGA-AO-A0J9-01 TCGA-A8-A07E-01 TCGA-A1-A0SE-01 TCGA-E9-A3HO-01 TCGA-A8-A091-01 TCGA-D8-A1XT-01 TCGA-AR-A1AQ-01 TCGA-MS-A51U-01 TCGA-AC-A6IX-01 TCGA-PL-A8LY-01 TCGA-A2-A0YD-01 TCGA-A8-A094-01 TCGA-D8-A1XJ-01 TCGA-BH-A0DG-01 TCGA-4H-AAAK-01 TCGA-AC-A5EI-01 TCGA-E2-A14S-01 TCGA-A8-A06O-01 TCGA-BH-A209-01 TCGA-AR-A24S-01 TCGA-A2-A3KD-01 TCGA-D8-A1JM-01 TCGA-A8-A08P-01 TCGA-E2-A15K-01 TCGA-AC-A2FK-01 TCGA-E9-A226-01 TCGA-E2-A1AZ-01 TCGA-D8-A1X8-01 TCGA-BH-A0EI-01 TCGA-C8-A1HO-01 TCGA-C8-A1HM-01 TCGA-AN-A0XR-01 TCGA-AN-A0FK-01 TCGA-E9-A1RA-01 TCGA-BH-A0HA-01 TCGA-OL-A6VR-01 TCGA-LL-A740-01 TCGA-A8-A097-01 TCGA-BH-A0BZ-01 TCGA-S3-A6ZG-01 TCGA-E9-A1NG-01 TCGA-AN-A0XP-01 TCGA-AO-A0J5-01 TCGA-A2-A0EM-01 TCGA-A8-A08T-01 TCGA-AC-A6NO-01 TCGA-A2-A0CO-01 TCGA-A2-A0YI-01 TCGA-AN-A0FZ-01 TCGA-BH-A0H6-01 TCGA-BH-A0BM-01 TCGA-AN-A0XW-01 TCGA-D8-A1XO-01 TCGA-EW-A1OV-01 TCGA-BH-A1EX-01 TCGA-A2-A04U-01 TCGA-C8-A26W-01 TCGA-A2-A0YM-01 TCGA-BH-A0DP-01 TCGA-GM-A2DF-01 TCGA-AR-A2LN-01 TCGA-D8-A1JF-01 TCGA-OL-A6VQ-01 TCGA-A2-A25F-01 TCGA-EW-A6SC-01 TCGA-E2-A1LL-01 TCGA-C8-A273-01 TCGA-E2-A153-01 TCGA-A8-A0A1-01 TCGA-D8-A27E-01 TCGA-A7-A0CJ-01 TCGA-AR-A24W-01 TCGA-E2-A9RU-01 TCGA-AR-A0TT-01 TCGA-C8-A132-01 TCGA-E2-A10F-01 TCGA-D8-A1JJ-01 TCGA-C8-A130-01 TCGA-E2-A1B4-01 TCGA-A8-A0A4-01 TCGA-D8-A1JH-01 TCGA-S3-AA0Z-01 TCGA-LL-A73Z-01 TCGA-EW-A1IZ-01 TCGA-C8-A1HI-01 TCGA-B6-A0RQ-01 TCGA-OL-A66N-01 TCGA-A7-A4SC-01 TCGA-AR-A2LH-01 TCGA-LL-A6FR-01 TCGA-LL-A5YO-01 TCGA-E9-A1N3-01 TCGA-A8-A08Z-01 TCGA-PL-A8LV-01 TCGA-AN-A0AL-01 TCGA-E9-A24A-01 TCGA-AC-A3QQ-01 TCGA-Z7-A8R5-01 TCGA-B6-A400-01 TCGA-BH-A0B9-01 TCGA-E2-A15T-01 TCGA-D8-A1X7-01 TCGA-E9-A247-01 TCGA-3C-AALI-01 TCGA-AO-A03U-01 TCGA-A8-A075-01 TCGA-AN-A041-01 TCGA-E9-A3Q9-01 TCGA-BH-A0E1-01 TCGA-BH-A0DL-01 TCGA-A1-A0SD-01 TCGA-C8-A12T-01 TCGA-E2-A158-01 TCGA-AR-A0TV-01 TCGA-AC-A2FM-01 TCGA-C8-A1HF-01 TCGA-A8-A079-01 TCGA-A2-A04Y-01 TCGA-BH-A204-01 TCGA-B6-A0WW-01 TCGA-BH-A0B4-01 TCGA-AC-A3OD-01 TCGA-E2-A154-01 TCGA-OL-A5RZ-01 TCGA-E2-A156-01 TCGA-A8-A07F-01 TCGA-AR-A24R-01 TCGA-D8-A1JL-01 TCGA-A2-A3XZ-01 TCGA-B6-A0RN-01 TCGA-A1-A0SP-01 TCGA-A2-A3Y0-01 TCGA-AC-A3YI-01 TCGA-A7-A0DB-01 TCGA-EW-A6SD-01 TCGA-A7-A426-01 TCGA-B6-A0RH-01 TCGA-BH-A6R8-01 TCGA-D8-A1JP-01 TCGA-A8-A07W-01 TCGA-E9-A1N6-01 TCGA-AR-A1AX-01 TCGA-E2-A14W-01 TCGA-AN-A0FS-01 TCGA-AR-A1AV-01 TCGA-EW-A1PA-01 TCGA-AC-A3TM-01 TCGA-D8-A27H-01 TCGA-C8-A12K-01 TCGA-AR-A2LE-01 TCGA-EW-A1PG-01 TCGA-AR-A1AS-01 TCGA-BH-A0HK-01 TCGA-GM-A4E0-01 TCGA-AO-A124-01 TCGA-S3-A6ZF-01 TCGA-D8-A1JC-01 TCGA-A8-A09D-01 TCGA-LD-A7W5-01 TCGA-A2-A3XS-01 TCGA-AR-A256-01 TCGA-A8-A095-01 TCGA-EW-A1OW-01 TCGA-AN-A0XO-01 TCGA-BH-A0DQ-01 TCGA-BH-A0BL-01 TCGA-AR-A1AI-01 TCGA-AR-A250-01 TCGA-A2-A0T3-01 TCGA-C8-A137-01 TCGA-D8-A1JG-01 TCGA-AR-A0TZ-01 TCGA-E2-A152-01 TCGA-AN-A0XV-01 TCGA-BH-A0HN-01 TCGA-AC-A2FE-01 TCGA-C8-A1HN-01 TCGA-AR-A24V-01 TCGA-AN-A0XS-01 TCGA-AO-A0J7-01 TCGA-OL-A66O-01 TCGA-A2-A0CR-01 TCGA-D8-A1XY-01 TCGA-A2-A0D1-01 TCGA-E2-A1L8-01 TCGA-BH-A0HF-01 TCGA-AN-A0FX-01 TCGA-E2-A1LG-01 TCGA-A8-A07Z-01 TCGA-AC-A62V-01 TCGA-A2-A0CK-01 TCGA-A7-A4SB-01 TCGA-AO-A0J3-01 TCGA-BH-A0AZ-01 TCGA-AO-A126-01 TCGA-AC-A8OR-01 TCGA-A2-A0YH-01 TCGA-AR-A1AO-01 TCGA-AN-A0FT-01 TCGA-A8-A09B-01 TCGA-GM-A3XL-01 TCGA-C8-A275-01 TCGA-AN-A0XU-01 TCGA-AO-A129-01 TCGA-AO-A03P-01 TCGA-BH-A0DS-01 TCGA-D8-A1X6-01 TCGA-EW-A3U0-01 TCGA-AQ-A7U7-01 TCGA-A2-A25A-01 TCGA-A7-A0CH-01 TCGA-AO-A12E-01 TCGA-E2-A10A-01 TCGA-C8-A1HK-01 TCGA-E9-A1R5-01 TCGA-E9-A54Y-01 TCGA-E9-A243-01 TCGA-E9-A2JS-01 TCGA-A2-A25D-01 TCGA-EW-A1J3-01 TCGA-BH-A1F8-01 TCGA-E2-A159-01 TCGA-C8-A12P-01 TCGA-A8-A0A7-01 TCGA-AQ-A54N-01 TCGA-A2-A04X-01 TCGA-D8-A27F-01 TCGA-A7-A0CD-01 TCGA-D8-A1JK-01 TCGA-B6-A0WV-01 TCGA-E2-A1LI-01 TCGA-GM-A5PX-01 TCGA-A8-A08X-01 TCGA-A7-A13F-01 TCGA-UL-AAZ6-01 TCGA-B6-A0RG-01 TCGA-BH-A0B5-01 TCGA-B6-A0RE-01 TCGA-BH-A208-01 TCGA-B6-A0WS-01 TCGA-BH-A1F6-01 TCGA-C8-A138-01 TCGA-BH-A0DO-01 TCGA-D8-A73U-01 TCGA-D8-A27N-01 TCGA-D8-A1X9-01 TCGA-AR-A0TR-01 TCGA-A8-A099-01 TCGA-LL-A8F5-01 TCGA-A7-A0DC-01 TCGA-E2-A14Z-01 TCGA-E9-A1NE-01 TCGA-A7-A56D-01 TCGA-AC-A3QP-01 TCGA-GM-A2DD-01 TCGA-EW-A1PH-01 TCGA-BH-A6R9-01 TCGA-C8-A8HP-01 TCGA-AR-A24X-01 TCGA-D8-A1Y0-01 TCGA-B6-A0IO-01 TCGA-A8-A07B-01 TCGA-AC-A2B8-01 TCGA-A8-A09A-01 TCGA-LL-A6FQ-01 TCGA-BH-A1FM-01 TCGA-A8-A086-01 TCGA-AR-A251-01 TCGA-BH-A202-01 TCGA-BH-A0DH-01 TCGA-UU-A93S-01 TCGA-E2-A1IE-01 TCGA-AR-A1AR-01 TCGA-AO-A1KT-01 TCGA-AN-A0FN-01 TCGA-AR-A24P-01 TCGA-OL-A5RY-01 TCGA-E9-A22H-01 TCGA-D8-A3Z6-01 TCGA-E2-A155-01 TCGA-A8-A09X-01 TCGA-A8-A08J-01 TCGA-B6-A0X1-01 TCGA-B6-A0RI-01 TCGA-AN-A0AJ-01 TCGA-A7-A26I-01 TCGA-AO-A128-01 TCGA-AR-A24T-01 TCGA-A8-A08O-01 TCGA-A8-A07U-01 TCGA-E9-A1N4-01 TCGA-A2-A0CT-01 TCGA-B6-A0RL-01 TCGA-BH-A1F2-01 TCGA-E9-A1N9-01 TCGA-B6-A0I9-01 TCGA-GM-A2DM-01 TCGA-A2-A4RY-01 TCGA-S3-A6ZH-01 TCGA-C8-A12V-01 TCGA-EW-A1PF-01 TCGA-E2-A1L9-01 TCGA-E2-A14Q-01 TCGA-A7-A26E-01 TCGA-AO-A03L-01 TCGA-D8-A1J9-01 TCGA-A2-A0SY-01 TCGA-E9-A1NF-01 TCGA-AC-A8OP-01 TCGA-AO-A03N-01 TCGA-A2-A3XU-01 TCGA-A7-A6VY-01 TCGA-AN-A0FY-01 TCGA-A2-A4S2-01 TCGA-AR-A1AP-01 TCGA-EW-A1PC-01 TCGA-GM-A2DA-01 TCGA-BH-A0HO-01 TCGA-EW-A6SB-01 TCGA-AC-A7VC-01 TCGA-AR-A1AN-01 TCGA-E2-A150-01 TCGA-HN-A2OB-01 TCGA-D8-A141-01 TCGA-BH-A0H5-01 TCGA-GM-A5PV-01 TCGA-OK-A5Q2-01 TCGA-A7-A6VW-01 TCGA-EW-A2FV-01 TCGA-E9-A1R3-01 TCGA-E2-A1IN-01 TCGA-AR-A254-01 TCGA-E2-A1LB-01 TCGA-BH-A18T-01 TCGA-A8-A07G-01 TCGA-E9-A54X-01 TCGA-BH-A0AV-01 TCGA-D8-A1JN-01 TCGA-A2-A0D0-01 TCGA-AO-A0JB-01 TCGA-A2-A25E-01 TCGA-AC-A3W7-01 TCGA-EW-A2FR-01 TCGA-C8-A133-01 TCGA-A2-A1G1-01 TCGA-AC-A3W5-01 TCGA-BH-A0BD-01 TCGA-E2-A1LK-01 TCGA-BH-A0HL-01 TCGA-EW-A3E8-01 TCGA-OL-A5RU-01 TCGA-A2-A0CP-01 TCGA-A7-A13G-01 TCGA-A2-A0SU-01 TCGA-E2-A1IH-01 TCGA-EW-A1IY-01 TCGA-B6-A0X4-01 TCGA-E9-A1NC-01 TCGA-D8-A1XQ-01 TCGA-A7-A0DA-01 TCGA-AC-A3HN-01 TCGA-BH-A0HB-01 TCGA-BH-A0H7-01 TCGA-A2-A0CL-01 TCGA-AC-A6IW-01 TCGA-EW-A1J5-01 TCGA-C8-A3M7-01 TCGA-AO-A0J6-01 TCGA-C8-A274-01 TCGA-C8-A27A-01 TCGA-AR-A1AK-01 TCGA-AC-A3EH-01 TCGA-B6-A0WZ-01 TCGA-BH-A5IZ-01 TCGA-LL-A73Y-01 TCGA-D8-A1Y3-01 TCGA-E2-A14V-01 TCGA-D8-A1Y1-01 TCGA-D8-A1JE-01 TCGA-AO-A03V-01 TCGA-E2-A105-01 TCGA-BH-A0E2-01 TCGA-BH-A0BJ-01 TCGA-BH-A203-01 TCGA-A8-A06U-01 TCGA-E9-A1R7-01 TCGA-E2-A10E-01 TCGA-E9-A249-01 TCGA-A2-A3XY-01 TCGA-A2-A04N-01 TCGA-C8-A1HE-01 TCGA-D8-A73W-01 TCGA-A2-A0ET-01 TCGA-AO-A0JI-01 TCGA-A8-A07P-01 TCGA-E9-A245-01 TCGA-OL-A6VO-01 TCGA-5L-AAT0-01 TCGA-AC-A23E-01 TCGA-E2-A1LA-01 TCGA-B6-A0X0-01 TCGA-D8-A145-01 TCGA-A2-A0CW-01 TCGA-A2-A0CU-01 TCGA-BH-A0C7-01 TCGA-B6-A0RM-01 TCGA-BH-A0HP-01 TCGA-B6-A0I8-01 TCGA-E2-A1L7-01 TCGA-A2-A0YE-01 TCGA-BH-A8FZ-01 TCGA-S3-AA17-01 TCGA-B6-A0IH-01 TCGA-C8-A12W-01 TCGA-D8-A13Z-01 TCGA-D8-A27K-01 TCGA-EW-A1J1-01 TCGA-AQ-A0Y5-01 TCGA-A8-A09W-01 TCGA-AC-A23C-01 TCGA-A2-A0EN-01 TCGA-EW-A1PB-01 TCGA-A7-A6VX-01 TCGA-E2-A108-01 TCGA-E9-A1N8-01 TCGA-A8-A085-01 TCGA-E2-A574-01 TCGA-E2-A1IG-01 TCGA-C8-A8HR-01 TCGA-E9-A1NH-01 TCGA-BH-A0E7-01 TCGA-AR-A24Q-01 TCGA-BH-A1F0-01 TCGA-A8-A06Q-01 TCGA-AR-A0U0-01 TCGA-AC-A5EH-01 TCGA-EW-A2FW-01 TCGA-E9-A1R0-01 TCGA-B6-A2IU-01 TCGA-E9-A1R2-01 TCGA-E9-A3X8-01 TCGA-AR-A255-01 TCGA-AO-A0JD-01 TCGA-A8-A08L-01 TCGA-AN-A0XL-01 TCGA-D8-A3Z5-01 TCGA-AR-A1AT-01 TCGA-AN-A03X-01 TCGA-B6-A0RO-01 TCGA-E9-A1NA-01 TCGA-AO-A0J8-01 TCGA-A8-A08R-01 TCGA-BH-A0DZ-01 TCGA-EW-A1PD-01 TCGA-E9-A1N5-01 TCGA-D8-A1J8-01 TCGA-A7-A0CE-01 TCGA-A2-A0D4-01 TCGA-A2-A0YC-01 TCGA-GM-A2DC-01 TCGA-AR-A24N-01 TCGA-E2-A1B0-01 TCGA-EW-A1IW-01 TCGA-EW-A6S9-01 TCGA-A2-A0CQ-01 TCGA-GM-A2DN-01 TCGA-AO-A03M-01 TCGA-A2-A3XT-01 TCGA-AQ-A1H3-01 TCGA-B6-A1KI-01 TCGA-B6-A0IQ-01 TCGA-AO-A1KS-01 TCGA-BH-A1FG-01 TCGA-AR-A0TS-01 TCGA-EW-A1P7-01 TCGA-BH-A18R-01 TCGA-E2-A1IL-01 TCGA-A7-A3IZ-01 TCGA-A2-A0CM-01 TCGA-AN-A04C-01 TCGA-A2-A04W-01 TCGA-AC-A4ZE-01 TCGA-A8-A06X-01 TCGA-D8-A143-01 TCGA-C8-A134-01 TCGA-A2-A0D2-01 TCGA-A2-A1G0-01 TCGA-AR-A24H-01 TCGA-AR-A2LQ-01 TCGA-A2-A0EP-01 TCGA-C8-A12Y-01 TCGA-A2-A0YT-01 TCGA-A8-A06T-01 TCGA-E9-A1R6-01 TCGA-D8-A1XZ-01 TCGA-BH-A0H3-01 TCGA-AR-A0TY-01 TCGA-E9-A248-01 TCGA-A2-A0SW-01 TCGA-E2-A1B6-01 TCGA-PE-A5DE-01 TCGA-A2-A0ST-01 TCGA-AC-A2BM-01 TCGA-BH-A0WA-01 TCGA-B6-A40C-01 TCGA-BH-A0EA-01 TCGA-A2-A0CZ-01 TCGA-C8-A12Q-01 TCGA-BH-AB28-01 TCGA-A8-A09N-01 TCGA-A2-A25C-01 TCGA-OL-A5DA-01 TCGA-E2-A15A-01 TCGA-A7-A5ZV-01 TCGA-LL-A50Y-01 TCGA-B6-A0WX-01 TCGA-A2-A04Q-01 TCGA-BH-A0E0-01 TCGA-E9-A2JT-01 TCGA-A2-A4S3-01 TCGA-E2-A15G-01 TCGA-BH-A1EO-01 TCGA-C8-A12U-01 TCGA-BH-A0HQ-01 TCGA-E2-A3DX-01 TCGA-A8-A09R-01 TCGA-E2-A107-01 TCGA-A8-A076-01 TCGA-B6-A0WT-01 TCGA-D8-A1Y2-01 TCGA-BH-A0BP-01 TCGA-C8-A131-01 TCGA-D8-A1JA-01 TCGA-AN-A0AR-01 TCGA-E2-A1L6-01 TCGA-A2-A0EO-01 TCGA-BH-A0BV-01 TCGA-D8-A27G-01 TCGA-E2-A109-01 TCGA-B6-A0I2-01 TCGA-AC-A5XS-01 TCGA-E2-A1IF-01 TCGA-AC-A2FO-01 TCGA-BH-A0C1-01 TCGA-B6-A1KF-01 TCGA-BH-A1FL-01 TCGA-A8-A06P-01 TCGA-AR-A1AY-01 TCGA-BH-A0AY-01 TCGA-AO-A0JG-01 TCGA-D8-A1XC-01 TCGA-AO-A0JE-01 TCGA-AC-A62X-01 TCGA-S3-AA11-01 TCGA-A8-A07R-01 TCGA-D8-A73X-01 TCGA-AN-A03Y-01 TCGA-A2-A0T7-01 TCGA-E9-A22G-01 TCGA-A2-A0CV-01 TCGA-D8-A27M-01 TCGA-A8-A081-01 TCGA-BH-A0RX-01 TCGA-C8-A135-01 TCGA-BH-A1FH-01 TCGA-BH-A1FJ-01 TCGA-BH-A0DV-01 TCGA-AO-A03O-01 TCGA-AC-A2QJ-01 TCGA-EW-A1PE-01 TCGA-B6-A0IN-01 TCGA-A7-A2KD-01 TCGA-E2-A1II-01 TCGA-D8-A27I-01 TCGA-S3-AA14-01 TCGA-A8-A08H-01 TCGA-B6-A3ZX-01 TCGA-B6-A0IP-01 TCGA-AR-A5QP-01 TCGA-AN-A0XN-01 TCGA-A1-A0SK-01 TCGA-E9-A6HE-01 TCGA-E9-A1NI-01 TCGA-LL-A441-01 TCGA-AO-A125-01 TCGA-A8-A0A2-01 TCGA-BH-A0HI-01 TCGA-AR-A252-01 TCGA-PE-A5DC-01 TCGA-D8-A142-01 TCGA-GM-A2DO-01 TCGA-LD-A9QF-01 TCGA-AR-A0U2-01 TCGA-E2-A15L-01 TCGA-BH-A0AU-01 TCGA-A2-A0T1-01 TCGA-A8-A07C-01 TCGA-A2-A0CS-01 TCGA-EW-A1P1-01 TCGA-OL-A66P-01 TCGA-B6-A1KC-01 TCGA-E9-A5UP-01 TCGA-A2-A1G4-01 TCGA-AR-A24L-01 TCGA-A2-A0D3-01 TCGA-BH-A1ET-01 TCGA-AO-A12G-01 TCGA-AO-A0JA-01 TCGA-BH-A0DX-01 TCGA-AR-A0TX-01 TCGA-A2-A1FV-01 TCGA-LD-A74U-01 TCGA-B6-A0RU-01 TCGA-GM-A2DB-01 TCGA-E9-A1ND-01 TCGA-E2-A15H-01 TCGA-E2-A15J-01 TCGA-E9-A244-01 TCGA-BH-A0B0-01 TCGA-A8-A093-01 TCGA-GM-A2DL-01 TCGA-EW-A1J6-01 TCGA-A8-A0AB-01 TCGA-A7-A26H-01 TCGA-AQ-A54O-01 TCGA-BH-A1FC-01 TCGA-E9-A22B-01 TCGA-A2-A3XV-01 TCGA-BH-A18V-01 TCGA-A2-A0EV-01 TCGA-D8-A1JT-01 TCGA-A2-A04P-01 TCGA-XX-A899-01 TCGA-BH-A18S-01 TCGA-E9-A228-01 TCGA-B6-A0WY-01 TCGA-E9-A1R4-01 TCGA-A8-A08A-01 TCGA-EW-A423-01 TCGA-AN-A04A-01 TCGA-EW-A1J2-01 TCGA-BH-A0GY-01 TCGA-W8-A86G-01 TCGA-A7-A5ZW-01 TCGA-E2-A56Z-01 TCGA-B6-A0IB-01 TCGA-C8-A27B-01 TCGA-A8-A096-01 TCGA-A7-A13E-01 TCGA-A2-A1G6-01 TCGA-A7-A26J-01 TCGA-E2-A14O-01 TCGA-AN-A0AS-01 TCGA-C8-A12X-01 TCGA-A7-A0D9-01 TCGA-D8-A4Z1-01 TCGA-D8-A1XL-01 TCGA-E9-A5UO-01 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TCGA-A8-A082-01 TCGA-3C-AALJ-01 TCGA-A8-A08G-01 TCGA-A7-A26G-01 TCGA-A2-A0YJ-01 TCGA-BH-A0BQ-01 TCGA-A2-A3KC-01 TCGA-OL-A66L-01 TCGA-AR-A2LM-01 TCGA-E2-A10C-01 TCGA-JL-A3YX-01 TCGA-AR-A0U1-01 TCGA-A8-A06N-01 TCGA-C8-A26V-01 TCGA-EW-A1IX-01 TCGA-E2-A1IJ-01 TCGA-LL-A440-01 TCGA-AR-A2LK-01 TCGA-OL-A66I-01 TCGA-AR-A0TW-01 TCGA-B6-A0I1-01 TCGA-BH-A8G0-01 TCGA-B6-A401-01 TCGA-BH-A0H9-01 TCGA-AO-A03R-01 TCGA-D8-A1XD-01 TCGA-AN-A0AM-01 TCGA-A2-A04V-01 TCGA-C8-A1HJ-01 TCGA-BH-A0W5-01 TCGA-AO-A12H-01 TCGA-BH-A0DK-01 TCGA-B6-A1KN-01 TCGA-BH-A0DI-01 TCGA-A7-A13D-01 TCGA-E2-A15S-01 TCGA-AR-A24K-01 TCGA-E9-A1RI-01 TCGA-GM-A2DI-01 TCGA-A2-A0T6-01 TCGA-EW-A1OZ-01 TCGA-BH-A0B7-01 TCGA-S3-AA12-01 TCGA-A2-A1FX-01 TCGA-BH-A0BG-01 TCGA-A7-A4SD-01 TCGA-A8-A09T-01 TCGA-B6-A0RV-01 TCGA-A7-A0CG-01 TCGA-AQ-A1H2-01 TCGA-D8-A27T-01 TCGA-BH-A1EW-01 TCGA-AR-A24O-01 TCGA-BH-A0HY-01 TCGA-E2-A15I-01 TCGA-C8-A278-01 TCGA-A2-A0EU-01 TCGA-BH-A1FE-01 TCGA-A8-A09C-01 TCGA-BH-A18L-01 TCGA-A1-A0SG-01 TCGA-A2-A0EX-01 TCGA-WT-AB41-01 TCGA-LL-A5YL-01 TCGA-D8-A1XR-01 TCGA-AR-A0TQ-01 TCGA-AN-A0AT-01 TCGA-A8-A0AD-01 TCGA-C8-A26X-01 TCGA-BH-A0E9-01 TCGA-E9-A22A-01 TCGA-A7-A3J1-01 TCGA-BH-A0BO-01 TCGA-AC-A3YJ-01 TCGA-A2-A0EQ-01 TCGA-D8-A1XW-01 TCGA-AN-A0FL-01 TCGA-BH-A18P-01 TCGA-PL-A8LZ-01 TCGA-LL-A5YP-01 TCGA-E2-A1B5-01 TCGA-AC-A2BK-01 TCGA-E2-A1BD-01 TCGA-BH-A0DE-01 TCGA-E2-A15O-01 TCGA-LD-A7W6-01 TCGA-BH-A0E6-01 TCGA-AO-A0JM-01 TCGA-D8-A1XM-01 TCGA-AC-A7VB-01 TCGA-E2-A14P-01 TCGA-E9-A227-01 TCGA-AN-A0AK-01 TCGA-BH-A1EU-01 TCGA-OL-A5D7-01 TCGA-OL-A97C-01 TCGA-PE-A5DD-01 TCGA-A2-A04R-01 TCGA-BH-A0B3-01 TCGA-D8-A1JS-01 TCGA-B6-A40B-01 TCGA-WT-AB44-01 TCGA-EW-A424-01 TCGA-BH-A1FR-01 TCGA-A7-A425-01 TCGA-B6-A0IK-01 TCGA-AR-A24U-01 TCGA-B6-A0IM-01 TCGA-E9-A1RF-01 TCGA-B6-A408-01 TCGA-BH-A18G-01 TCGA-BH-A0EE-01 TCGA-E2-A15E-01 TCGA-A8-A090-01 TCGA-5T-A9QA-01 TCGA-A8-A08B-01 TCGA-AN-A0XT-01 TCGA-AC-A2FG-01 TCGA-AO-A0J2-01 TCGA-AR-A1AL-01 TCGA-A8-A09G-01 TCGA-BH-A28Q-01 TCGA-C8-A1HG-01 TCGA-D8-A1XK-01 TCGA-A7-A4SA-01 TCGA-3C-AAAU-01 TCGA-AO-A0J4-01 TCGA-AC-A2FB-01 TCGA-AC-A8OQ-01 TCGA-D8-A1JU-01 TCGA-C8-A12L-01 TCGA-BH-A0BT-01 TCGA-A2-A0YK-01 TCGA-A1-A0SO-01 TCGA-B6-A0IA-01 TCGA-EW-A6SA-01 TCGA-BH-A0C3-01
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initial_data/brca_tcga_pan_can_atlas_2018/case_lists/cases_sv.txt
ADDED
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+
cancer_study_identifier: brca_tcga_pan_can_atlas_2018
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| 2 |
+
stable_id: brca_tcga_pan_can_atlas_2018_sv
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| 3 |
+
case_list_name: Samples with SV data
|
| 4 |
+
case_list_description: All samples
|
| 5 |
+
case_list_category: all_cases_with_sv_data
|
| 6 |
+
case_list_ids: TCGA-OL-A66H-01 TCGA-3C-AALK-01 TCGA-AR-A1AH-01 TCGA-AR-A1AJ-01 TCGA-AC-A62Y-01 TCGA-E9-A1QZ-01 TCGA-E2-A10B-01 TCGA-C8-A1HL-01 TCGA-EW-A2FS-01 TCGA-D8-A1XA-01 TCGA-AO-A1KQ-01 TCGA-A8-A0A6-01 TCGA-B6-A0IE-01 TCGA-GM-A2D9-01 TCGA-AQ-A04J-01 TCGA-E9-A1RD-01 TCGA-LD-A66U-01 TCGA-BH-A1EN-01 TCGA-BH-A1FN-01 TCGA-E2-A15R-01 TCGA-E9-A3QA-01 TCGA-BH-A0H0-01 TCGA-A2-A3XX-01 TCGA-BH-A0EB-01 TCGA-GM-A2DK-01 TCGA-BH-A1EY-01 TCGA-AC-A8OS-01 TCGA-BH-A18K-01 TCGA-A7-A4SE-01 TCGA-BH-A0DT-01 TCGA-AC-A6IV-01 TCGA-LL-A7SZ-01 TCGA-A1-A0SJ-01 TCGA-AR-A2LJ-01 TCGA-D8-A1X5-01 TCGA-D8-A1JB-01 TCGA-BH-A0BC-01 TCGA-AN-A0G0-01 TCGA-AO-A03T-01 TCGA-D8-A27P-01 TCGA-D8-A1JD-01 TCGA-E2-A570-01 TCGA-OL-A66J-01 TCGA-AR-A2LO-01 TCGA-E9-A5FL-01 TCGA-BH-A201-01 TCGA-LL-A5YM-01 TCGA-A2-A0T2-01 TCGA-AR-A0TP-01 TCGA-EW-A1P0-01 TCGA-A2-A4RW-01 TCGA-D8-A1XV-01 TCGA-A7-A3RF-01 TCGA-D8-A13Y-01 TCGA-AR-A0TU-01 TCGA-A8-A07L-01 TCGA-A8-A07I-01 TCGA-D8-A1JI-01 TCGA-E2-A15P-01 TCGA-OL-A5RX-01 TCGA-A2-A0EY-01 TCGA-BH-A0B8-01 TCGA-XX-A89A-01 TCGA-EW-A1OY-01 TCGA-B6-A0RP-01 TCGA-LL-A9Q3-01 TCGA-A1-A0SQ-01 TCGA-AR-A5QM-01 TCGA-D8-A27V-01 TCGA-EW-A1P5-01 TCGA-BH-A18N-01 TCGA-AC-A23H-01 TCGA-BH-A0B1-01 TCGA-AN-A0FW-01 TCGA-A2-A1FZ-01 TCGA-A2-A0SV-01 TCGA-BH-A0BA-01 TCGA-E2-A2P6-01 TCGA-B6-A0RT-01 TCGA-D8-A27R-01 TCGA-C8-A26Z-01 TCGA-BH-A1FU-01 TCGA-E2-A14Y-01 TCGA-AO-A1KO-01 TCGA-OL-A5D6-01 TCGA-AO-A0J9-01 TCGA-A8-A07E-01 TCGA-A1-A0SE-01 TCGA-E9-A3HO-01 TCGA-A8-A091-01 TCGA-D8-A1XT-01 TCGA-AR-A1AQ-01 TCGA-MS-A51U-01 TCGA-AC-A6IX-01 TCGA-PL-A8LY-01 TCGA-A2-A0YD-01 TCGA-A8-A094-01 TCGA-D8-A1XJ-01 TCGA-BH-A0DG-01 TCGA-4H-AAAK-01 TCGA-AC-A5EI-01 TCGA-E2-A14S-01 TCGA-A8-A06O-01 TCGA-BH-A209-01 TCGA-AR-A24S-01 TCGA-A2-A3KD-01 TCGA-D8-A1JM-01 TCGA-A8-A08P-01 TCGA-E2-A15K-01 TCGA-AC-A2FK-01 TCGA-E9-A226-01 TCGA-E2-A1AZ-01 TCGA-D8-A1X8-01 TCGA-BH-A0EI-01 TCGA-C8-A1HO-01 TCGA-C8-A1HM-01 TCGA-AN-A0XR-01 TCGA-AN-A0FK-01 TCGA-E9-A1RA-01 TCGA-BH-A0HA-01 TCGA-OL-A6VR-01 TCGA-LL-A740-01 TCGA-A8-A097-01 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TCGA-AN-A0FV-01 TCGA-A8-A06R-01 TCGA-E2-A1LS-01 TCGA-BH-A18U-01 TCGA-AO-A0JJ-01 TCGA-BH-A0C0-01 TCGA-AO-A1KP-01 TCGA-B6-A0X7-01 TCGA-A8-A09I-01 TCGA-E9-A1RE-01 TCGA-OL-A5RV-01 TCGA-E2-A1BC-01 TCGA-A2-A0YF-01 TCGA-E9-A22D-01 TCGA-A2-A3XW-01 TCGA-E2-A15F-01 TCGA-A1-A0SF-01 TCGA-A2-A0CX-01 TCGA-E9-A1RC-01 TCGA-AR-A1AU-01 TCGA-A7-A6VV-01 TCGA-BH-A0W7-01 TCGA-BH-A8FY-01 TCGA-E2-A15C-01 TCGA-V7-A7HQ-01 TCGA-D8-A27L-01 TCGA-AN-A046-01 TCGA-A2-A0ER-01 TCGA-BH-A0BW-01 TCGA-A8-A09V-01 TCGA-GM-A3NY-01 TCGA-BH-A5J0-01 TCGA-AR-A1AW-01 TCGA-AR-A24Z-01 TCGA-A1-A0SM-01 TCGA-C8-A12O-01 TCGA-BH-A0BR-01 TCGA-Z7-A8R6-01 TCGA-OL-A66K-01 TCGA-GI-A2C9-01 TCGA-B6-A0I6-01 TCGA-A2-A4S1-01 TCGA-BH-A42V-01 TCGA-E9-A5FK-01 TCGA-D8-A1XB-01 TCGA-AN-A0FD-01 TCGA-OL-A5D8-01 TCGA-A2-A0YL-01 TCGA-A7-A5ZX-01 TCGA-AQ-A04H-01 TCGA-AR-A5QQ-01 TCGA-D8-A1XG-01 TCGA-B6-A0RS-01 TCGA-AR-A0U3-01 TCGA-S3-AA15-01 TCGA-B6-A0IJ-01 TCGA-AO-A0JF-01 TCGA-A2-A0T0-01 TCGA-EW-A1OX-01 TCGA-S3-AA10-01 TCGA-C8-A8HQ-01 TCGA-BH-A0HW-01 TCGA-LL-A6FP-01 TCGA-A2-A0T5-01 TCGA-E2-A15M-01 TCGA-AC-A2QH-01 TCGA-B6-A0I5-01 TCGA-AR-A24M-01 TCGA-BH-A18I-01 TCGA-A2-A1FW-01 TCGA-A8-A083-01 TCGA-E2-A576-01 TCGA-GM-A3NW-01 TCGA-A8-A0A9-01 TCGA-E2-A573-01 TCGA-D8-A147-01 TCGA-BH-A1F5-01 TCGA-A7-A4SF-01 TCGA-D8-A140-01 TCGA-LL-A5YN-01 TCGA-AN-A04D-01 TCGA-B6-A402-01 TCGA-A2-A25B-01 TCGA-D8-A27W-01 TCGA-E2-A1IK-01 TCGA-BH-A1FB-01 TCGA-C8-A3M8-01 TCGA-E2-A1LE-01 TCGA-A8-A09Z-01 TCGA-A2-A0EW-01 TCGA-D8-A1XU-01 TCGA-A8-A07O-01 TCGA-A1-A0SI-01 TCGA-PL-A8LX-01 TCGA-E9-A1RH-01 TCGA-AO-A0JC-01 TCGA-A2-A04T-01 TCGA-BH-A0HU-01 TCGA-AC-A3TN-01 TCGA-E2-A1IO-01 TCGA-OL-A5S0-01 TCGA-C8-A26Y-01 TCGA-AN-A049-01 TCGA-E2-A14R-01 TCGA-GM-A2DH-01 TCGA-BH-A0AW-01 TCGA-A8-A07J-01 TCGA-E9-A229-01 TCGA-EW-A1P3-01 TCGA-BH-A1ES-01 TCGA-C8-A12N-01 TCGA-A2-A0SX-01 TCGA-BH-A1FD-01 TCGA-BH-A0BF-01 TCGA-AR-A5QN-01 TCGA-E2-A2P5-01 TCGA-B6-A0IC-01 TCGA-BH-A0DD-01 TCGA-E2-A1LH-01 TCGA-BH-A1EV-01 TCGA-BH-A0HX-01 TCGA-E2-A14N-01 TCGA-A2-A259-01 TCGA-E2-A1B1-01 TCGA-AN-A0FF-01 TCGA-A7-A3J0-01 TCGA-A8-A06Z-01 TCGA-OL-A5RW-01 TCGA-BH-A18M-01 TCGA-E9-A22E-01 TCGA-A8-A092-01 TCGA-HN-A2NL-01 TCGA-B6-A0X5-01 TCGA-D8-A1XS-01 TCGA-C8-A9FZ-01 TCGA-A8-A09M-01 TCGA-JL-A3YW-01 TCGA-A1-A0SH-01 TCGA-A1-A0SB-01 TCGA-BH-A0GZ-01 TCGA-BH-A18Q-01 TCGA-BH-A0W4-01 TCGA-BH-A2L8-01 TCGA-AO-A12B-01 TCGA-A2-A0ES-01 TCGA-AN-A0FJ-01 TCGA-E2-A14T-01 TCGA-AO-A12A-01 TCGA-AQ-A04L-01 TCGA-A1-A0SN-01 TCGA-E9-A295-01 TCGA-A8-A08I-01 TCGA-E2-A1IU-01 TCGA-AO-A0JL-01 TCGA-BH-A0BS-01 TCGA-EW-A1P8-01 TCGA-A8-A06Y-01 TCGA-GI-A2C8-01 TCGA-C8-A12Z-01 TCGA-AR-A0U4-01 TCGA-B6-A409-01 TCGA-A7-A26F-01 TCGA-B6-A0IG-01 TCGA-E2-A15D-01 TCGA-BH-A0B2-01 TCGA-E9-A1RB-01 TCGA-AO-A12F-01 TCGA-EW-A1P4-01 TCGA-AO-A12D-01 TCGA-AO-A1KR-01 TCGA-EW-A1P6-01 TCGA-D8-A1XF-01 TCGA-BH-A18F-01 TCGA-E2-A14X-01 TCGA-E9-A1RG-01 TCGA-AC-A5XU-01 TCGA-A2-A0YG-01 TCGA-A8-A09Q-01 TCGA-AC-A2FF-01 TCGA-A2-A0T4-01 TCGA-BH-A0W3-01 TCGA-BH-A18J-01 TCGA-LL-A7T0-01 TCGA-BH-A18H-01 TCGA-BH-A42U-01 TCGA-C8-A12M-01 TCGA-A8-A082-01 TCGA-3C-AALJ-01 TCGA-A8-A08G-01 TCGA-A7-A26G-01 TCGA-A2-A0YJ-01 TCGA-BH-A0BQ-01 TCGA-A2-A3KC-01 TCGA-OL-A66L-01 TCGA-AR-A2LM-01 TCGA-E2-A10C-01 TCGA-JL-A3YX-01 TCGA-AR-A0U1-01 TCGA-A8-A06N-01 TCGA-C8-A26V-01 TCGA-EW-A1IX-01 TCGA-E2-A1IJ-01 TCGA-LL-A440-01 TCGA-AR-A2LK-01 TCGA-OL-A66I-01 TCGA-AR-A0TW-01 TCGA-B6-A0I1-01 TCGA-BH-A8G0-01 TCGA-B6-A401-01 TCGA-BH-A0H9-01 TCGA-AO-A03R-01 TCGA-D8-A1XD-01 TCGA-AN-A0AM-01 TCGA-A2-A04V-01 TCGA-C8-A1HJ-01 TCGA-BH-A0W5-01 TCGA-AO-A12H-01 TCGA-BH-A0DK-01 TCGA-B6-A1KN-01 TCGA-BH-A0DI-01 TCGA-A7-A13D-01 TCGA-E2-A15S-01 TCGA-AR-A24K-01 TCGA-E9-A1RI-01 TCGA-GM-A2DI-01 TCGA-A2-A0T6-01 TCGA-EW-A1OZ-01 TCGA-BH-A0B7-01 TCGA-S3-AA12-01 TCGA-A2-A1FX-01 TCGA-BH-A0BG-01 TCGA-A7-A4SD-01 TCGA-A8-A09T-01 TCGA-B6-A0RV-01 TCGA-A7-A0CG-01 TCGA-AQ-A1H2-01 TCGA-D8-A27T-01 TCGA-BH-A1EW-01 TCGA-AR-A24O-01 TCGA-BH-A0HY-01 TCGA-E2-A15I-01 TCGA-C8-A278-01 TCGA-A2-A0EU-01 TCGA-BH-A1FE-01 TCGA-A8-A09C-01 TCGA-BH-A18L-01 TCGA-A1-A0SG-01 TCGA-A2-A0EX-01 TCGA-WT-AB41-01 TCGA-LL-A5YL-01 TCGA-D8-A1XR-01 TCGA-AR-A0TQ-01 TCGA-AN-A0AT-01 TCGA-A8-A0AD-01 TCGA-C8-A26X-01 TCGA-BH-A0E9-01 TCGA-E9-A22A-01 TCGA-A7-A3J1-01 TCGA-BH-A0BO-01 TCGA-AC-A3YJ-01 TCGA-A2-A0EQ-01 TCGA-D8-A1XW-01 TCGA-AN-A0FL-01 TCGA-BH-A18P-01 TCGA-PL-A8LZ-01 TCGA-LL-A5YP-01 TCGA-E2-A1B5-01 TCGA-AC-A2BK-01 TCGA-E2-A1BD-01 TCGA-BH-A0DE-01 TCGA-E2-A15O-01 TCGA-LD-A7W6-01 TCGA-BH-A0E6-01 TCGA-AO-A0JM-01 TCGA-D8-A1XM-01 TCGA-AC-A7VB-01 TCGA-E2-A14P-01 TCGA-E9-A227-01 TCGA-AN-A0AK-01 TCGA-BH-A1EU-01 TCGA-OL-A5D7-01 TCGA-OL-A97C-01 TCGA-PE-A5DD-01 TCGA-A2-A04R-01 TCGA-BH-A0B3-01 TCGA-D8-A1JS-01 TCGA-B6-A40B-01 TCGA-WT-AB44-01 TCGA-EW-A424-01 TCGA-BH-A1FR-01 TCGA-A7-A425-01 TCGA-B6-A0IK-01 TCGA-AR-A24U-01 TCGA-B6-A0IM-01 TCGA-E9-A1RF-01 TCGA-B6-A408-01 TCGA-BH-A18G-01 TCGA-BH-A0EE-01 TCGA-E2-A15E-01 TCGA-A8-A090-01 TCGA-5T-A9QA-01 TCGA-A8-A08B-01 TCGA-AN-A0XT-01 TCGA-AC-A2FG-01 TCGA-AO-A0J2-01 TCGA-AR-A1AL-01 TCGA-A8-A09G-01 TCGA-BH-A28Q-01 TCGA-C8-A1HG-01 TCGA-D8-A1XK-01 TCGA-A7-A4SA-01 TCGA-3C-AAAU-01 TCGA-AO-A0J4-01 TCGA-AC-A2FB-01 TCGA-AC-A8OQ-01 TCGA-D8-A1JU-01 TCGA-C8-A12L-01 TCGA-BH-A0BT-01 TCGA-A2-A0YK-01 TCGA-A1-A0SO-01 TCGA-B6-A0IA-01 TCGA-EW-A6SA-01 TCGA-BH-A0C3-01
|
initial_data/brca_tcga_pan_can_atlas_2018/normals/meta_mrna_seq_v2_rsem_normal_samples.txt
ADDED
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@@ -0,0 +1,8 @@
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| 1 |
+
cancer_study_identifier: brca_tcga_pan_can_atlas_2018
|
| 2 |
+
stable_id: rna_seq_v2_mrna_median_normals
|
| 3 |
+
genetic_alteration_type: MRNA_EXPRESSION
|
| 4 |
+
datatype: CONTINUOUS
|
| 5 |
+
show_profile_in_analysis_tab: FALSE
|
| 6 |
+
profile_name: mRNA expression of adjacent normal samples, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2)
|
| 7 |
+
profile_description:mRNA expression of adjacent normal samples, RSEM (Batch normalized from Illumina HiSeq_RNASeqV2)
|
| 8 |
+
data_filename: data_mrna_seq_v2_rsem_normal_samples.txt
|
initial_data/brca_tcga_pan_can_atlas_2018/normals/meta_mrna_seq_v2_rsem_normal_samples_zscores_ref_normal_samples.txt
ADDED
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@@ -0,0 +1,8 @@
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| 1 |
+
cancer_study_identifier: brca_tcga_pan_can_atlas_2018
|
| 2 |
+
genetic_alteration_type: MRNA_EXPRESSION
|
| 3 |
+
datatype: Z-SCORE
|
| 4 |
+
stable_id: rna_seq_v2_mrna_median_normals_Zscores
|
| 5 |
+
show_profile_in_analysis_tab: TRUE
|
| 6 |
+
profile_name: mRNA expression of adjacent normal samples, z-scores relative to all normal samples (log RNA Seq V2 RSEM)
|
| 7 |
+
profile_description: Expression z-scores of adjacent normal samples compared to the expression distribution of all log-transformed mRNA expression of adjacent normal samples in the cohort.
|
| 8 |
+
data_filename: data_mrna_seq_v2_rsem_normal_samples_zscores_ref_normal_samples.txt
|
initial_data/inductive_graph_residual_extension/architecture/INDUCTIVE_GR_DESIGN.md
ADDED
|
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|
| 1 |
+
# INDUCTIVE GR DESIGN
|
| 2 |
+
|
| 3 |
+
Status: design only. No module is implemented and no training is started.
|
| 4 |
+
|
| 5 |
+
## Proposed input/output contract
|
| 6 |
+
|
| 7 |
+
```text
|
| 8 |
+
protein sequence -> frozen ESM2 (or equivalent sequence featurizer) -> x_v
|
| 9 |
+
raw node features for v and permitted neighbors -> feature encoders
|
| 10 |
+
relation-typed edges (v, r, u) -> relation-aware message passing / aggregation
|
| 11 |
+
-> 64D inductive graph representation g_v
|
| 12 |
+
g_v -> existing 64 -> 256 -> 640 residual projector
|
| 13 |
+
ESM2_640 + beta * residual_640 -> existing LayerNorm/fusion path
|
| 14 |
+
```
|
| 15 |
+
|
| 16 |
+
The new encoder must be a function of node attributes and local relation-typed neighborhoods, not a function of the protein ID or a learned row in a fixed node table. A GraphSAGE/R-GCN-style layer stack with relation-specific transforms is a compatible design family; the exact layer count, aggregation, and normalization are intentionally not chosen in Phase 0.
|
| 17 |
+
|
| 18 |
+
## New component: required changes
|
| 19 |
+
|
| 20 |
+
1. Replace the current lookup-only graph input with a feature-to-64D node encoder. Minimum safe input is sequence-derived (`ESM2`, length, and/or AA composition); external GO/PTM/pathway features are optional and require a frozen, target-blind availability policy.
|
| 21 |
+
2. Add relation-aware message passing over only relations available at inference. The graph context for a test protein must be built after the test node is introduced; no test protein row or incident edge may be used to train the encoder.
|
| 22 |
+
3. Add a missing-context policy: sequence-only is a valid path, while absent relation context must not call the V2 `fallback(graph)` branch with a nonexistent tensor.
|
| 23 |
+
4. Define neighbor feature encoders for non-protein nodes if mutation/PTM/pathway/disease neighbors are used. Their features must also be computable for unseen neighbors; otherwise restrict the encoder to a node set with explicit feature contracts.
|
| 24 |
+
5. Use feature-aware batching/sampling and an explicit node-ID-independent inference API such as `encode_node(node_features, typed_neighbors) -> g_v_64`.
|
| 25 |
+
|
| 26 |
+
## Existing components that remain unchanged
|
| 27 |
+
|
| 28 |
+
- The current 64D-to-256D-to-640D residual projector can remain unchanged once its input is the new encoder's 64D output.
|
| 29 |
+
- The existing ESM2 640D branch, LayerNorm, scalar beta concept, residual preservation objective, and 640D relation scoring can remain as interfaces, subject to a new model's own training and calibration.
|
| 30 |
+
- Existing graph relation semantics and the six-forward/twelve-serialized relation inventory can remain only for relations that are genuinely available at inference; PPI target edges must stay excluded for PPI retrieval.
|
| 31 |
+
- The original lookup-based checkpoint and benchmark are not overwritten and are not silently reinterpreted as inductive.
|
| 32 |
+
|
| 33 |
+
## Feasibility verdict
|
| 34 |
+
|
| 35 |
+
**Architecture-level feasible, implementation-level not yet validated.** The dataset supplies sequence-derived features for the full proposed test set and has source relation inventories for all test proteins. However, a new inductive encoder and a strict feature/neighbor availability contract are required. Current Graph-Residual V2 cannot be extended by configuration alone.
|
initial_data/inductive_graph_residual_extension/audit/CURRENT_GR_V2_SPEC.md
ADDED
|
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|
| 1 |
+
# CURRENT GR V2 SPEC
|
| 2 |
+
|
| 3 |
+
Audit scope: static/read-only recovery on 2026-09-09T14:08:01.173504+00:00.
|
| 4 |
+
No training, source-model edit, benchmark edit, paper edit, or checkpoint creation was performed.
|
| 5 |
+
|
| 6 |
+
## Resolved sources
|
| 7 |
+
|
| 8 |
+
| item | path |
|
| 9 |
+
|---|---|
|
| 10 |
+
| recovered V2 model | `/root/autodl-tmp/bio/clinvar_strict_rebuild_v1/12_code_snapshot/recovered_v2/residual_v2/model.py` |
|
| 11 |
+
| current compatibility model | `/root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_model_benchmark_v3/dmptm_benchmark/models/residual_v2_compat/model.py` |
|
| 12 |
+
| recovered V2 data interface | `/root/autodl-tmp/bio/clinvar_strict_rebuild_v1/12_code_snapshot/recovered_v2/residual_v2/data.py` |
|
| 13 |
+
| V2 configuration | `/root/autodl-tmp/bio/clinvar_strict_rebuild_v1/12_code_snapshot/recovered_v2/config.server.yaml` |
|
| 14 |
+
| graph construction | `/root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/build_graph.py` |
|
| 15 |
+
| graph pretraining | `/root/autodl-tmp/bio/clinvar_strict_rebuild_v1/12_code_snapshot/recovered_graph_pretrain/dmptm_gcl/train_contrastive.py` |
|
| 16 |
+
| graph core | `/root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core` |
|
| 17 |
+
| exported 64D graph assets | `/root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_embedding_assets_v1` |
|
| 18 |
+
| archived V2 640D outputs | `/root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_esm2_residual_pretrain_v2` |
|
| 19 |
+
| ESM2 sequence assets used for coverage audit | `/root/autodl-tmp/bio/clinvar_strict_rebuild_v1/01_raw_manifest/esm2_only_v1/core_embeddings` |
|
| 20 |
+
|
| 21 |
+
## Architecture recovery
|
| 22 |
+
|
| 23 |
+
- Raw graph embedding dimension: **64D** for each of `disease`, `mutation`, `protein`, `ptm`, and `pathway`.
|
| 24 |
+
- The graph pretrainer uses per-node `nn.Embedding(count, hidden_dim, sparse=True)` tables, relation-specific linear projections, and node projections. It samples relation edges and uses in-batch contrastive negatives; it does not aggregate neighbor states.
|
| 25 |
+
- Graph construction serializes six forward relations plus six reverse relations: mutation–protein, protein–PTM, protein–pathway, disease–mutation, disease–PTM, and disease–protein. The core configuration explicitly says `uses_mutation_ptm_direct_edges: false`.
|
| 26 |
+
- V2 consumes the fixed 64D graph row through an MLP `64 -> 256 -> 640`. For sequence-bearing node types, the fused representation is `LayerNorm(ESM2_640 + beta * residual_MLP(graph_64))`. The trained V2 run records `beta=-0.05` at the safety clamp. Non-sequence disease/pathway rows use a graph projector with the same `64 -> 256 -> 640` dimensions.
|
| 27 |
+
- V2 also has a `fallback(graph)` MLP selected when the ESM validity mask is false. This is an invalid-sequence branch, not a missing-graph or unseen-node branch.
|
| 28 |
+
|
| 29 |
+
## Required answers
|
| 30 |
+
|
| 31 |
+
1. **Graph embedding source:** lookup-table-derived, learned during graph pretraining and exported as fixed row-indexed `.npy` arrays. The V2 module itself does not contain a raw-node graph encoder.
|
| 32 |
+
2. **Protein-ID dependence:** **YES**. The data interface indexes the graph array by the node index aligned to a `node_id` mapping. A protein absent from that mapping has no graph row.
|
| 33 |
+
3. **Message passing:** **NO** in the recovered graph pretrainer and V2 path. There is no neighbor aggregation, GNN layer, or `edge_index`-conditioned state update in the V2 model.
|
| 34 |
+
4. **Node feature encoder:** **NO**. Sequence ESM2 is supplied as a fixed input; the graph side receives a precomputed 64D row. No raw sequence/length/AA-composition/domain encoder is defined.
|
| 35 |
+
5. **Inductive pathway:** **NO**. There is no function that builds a graph representation for a new protein from raw node features and its neighbors. Missing graph input fails before the ESM validity fallback can make the call usable.
|
| 36 |
+
|
| 37 |
+
## Current V2 input consistency note
|
| 38 |
+
|
| 39 |
+
The recovered `data.py` expects `work/esm2_only_v1/core_embeddings` below its `root`, while the currently present canonical archived ESM2 assets resolved for this audit are under `/root/autodl-tmp/bio/clinvar_strict_rebuild_v1/01_raw_manifest/esm2_only_v1/core_embeddings`. The explicit archived ESM mapping is aligned to the graph protein mapping: `True`. This path mismatch is a reproducibility issue, not an inductive capability.
|
| 40 |
+
|
| 41 |
+
## Conclusion
|
| 42 |
+
|
| 43 |
+
**CURRENT MODEL: LOOKUP_BASED**. The current Graph-Residual V2 is transductive with respect to graph representations; its fixed 64D graph rows cannot be generated for a genuinely unseen protein.
|
initial_data/inductive_graph_residual_extension/audit/PHASE0_STATUS.tsv
ADDED
|
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|
|
|
|
|
|
|
|
|
|
| 1 |
+
check status detail
|
| 2 |
+
source_model_read PASS /root/autodl-tmp/bio/clinvar_strict_rebuild_v1/12_code_snapshot/recovered_v2/residual_v2/model.py
|
| 3 |
+
source_data_read PASS /root/autodl-tmp/bio/clinvar_strict_rebuild_v1/12_code_snapshot/recovered_v2/residual_v2/data.py
|
| 4 |
+
graph_construction_read PASS /root/autodl-tmp/bio/disease_mutation_ptm_gcl/dmptm_gcl/build_graph.py
|
| 5 |
+
protein_universe PASS 14231
|
| 6 |
+
esm_shape PASS (14231, 640)
|
| 7 |
+
esm_mapping_alignment PASS explicit node_id compare
|
| 8 |
+
sequence_valid_for_test PASS 2846/2846
|
| 9 |
+
protein_split_disjoint PASS intersection=0
|
| 10 |
+
training_started NO audit script has no training import or call
|
| 11 |
+
checkpoint_created NO no checkpoint output path used
|
| 12 |
+
benchmark_modified NO only new audit directory was written
|
initial_data/inductive_graph_residual_extension/audit/UNSEEN_NODE_CASES.tsv
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
case label visibility_view test proteins sequence neighbors relations node features notes
|
| 2 |
+
A sequence only strict train-graph view 2846 YES for 2846 NO (all test incident edges removed from training graph) NO in training graph; preserved only in held-out source snapshot sequence-derived YES; graph lookup NO All test proteins are graph-unseen during representation training. This is the sequence-only fallback regime.
|
| 3 |
+
B sequence + unseen neighbors held-out inference view with source relations revealed 2846 YES for 2846 YES for 2846 YES in held-out source snapshot; not visible during training sequence-derived YES; neighbor features CONDITIONAL All four relation types are reported by coverage below; current V2 cannot encode the new protein from them because it has no message passing.
|
| 4 |
+
C no information held-out inference view 0 NO NO NO NO No such test protein is present in the proposed split; this remains a valid future-data failure case.
|
initial_data/inductive_graph_residual_extension/audit/UNSEEN_NODE_RELATION_COVERAGE.tsv
ADDED
|
@@ -0,0 +1,5 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
relation test proteins with relation test coverage full graph edge count strict training visibility
|
| 2 |
+
mutation 2846 2846/2846 (100.0000%) 1055821 0 test-node incident edges
|
| 3 |
+
ptm 2846 2846/2846 (100.0000%) 166288 0 test-node incident edges
|
| 4 |
+
pathway 1810 1810/2846 (63.5980%) 119255 0 test-node incident edges
|
| 5 |
+
disease 2846 2846/2846 (100.0000%) 288376 0 test-node incident edges
|
initial_data/inductive_graph_residual_extension/audits/ENCODER_STATIC_SHAPE_TEST.md
ADDED
|
@@ -0,0 +1,14 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# Encoder static shape test
|
| 2 |
+
|
| 3 |
+
**Status: PASS**
|
| 4 |
+
|
| 5 |
+
- Synthetic unseen-protein batch: `4`
|
| 6 |
+
- Node feature shape: `(4, 661)` (661D contract vector, including the 640D ESM2 block)
|
| 7 |
+
- Neighbor feature shape: `(4, 3, 661)`
|
| 8 |
+
- Relation ID shape: `(4, 3)`
|
| 9 |
+
- Output shape: `(4, 64)`
|
| 10 |
+
- Node embedding lookup table loaded: `NO`
|
| 11 |
+
- Training started: `NO`
|
| 12 |
+
|
| 13 |
+
This is a forward shape check only. It creates no result checkpoint and does
|
| 14 |
+
not evaluate a biological task.
|
initial_data/inductive_graph_residual_extension/audits/FEATURE_LEAKAGE_AUDIT.md
ADDED
|
@@ -0,0 +1,35 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# Feature leakage audit
|
| 2 |
+
|
| 3 |
+
## Decision
|
| 4 |
+
|
| 5 |
+
**PASS**. The Phase 1 contract is locked to sequence-derived inputs only:
|
| 6 |
+
640D frozen ESM2, one protein-length scalar, and 20D amino-acid composition
|
| 7 |
+
(661 dimensions total). The same feature schema is available before
|
| 8 |
+
the protein split for all 14,231 proteins.
|
| 9 |
+
|
| 10 |
+
## Evidence
|
| 11 |
+
|
| 12 |
+
- ESM2 source asset: `/root/autodl-tmp/bio/clinvar_strict_rebuild_v1/01_raw_manifest/esm2_only_v1/core_embeddings/protein_esm2_embeddings.npy`
|
| 13 |
+
- ESM mapping: `/root/autodl-tmp/bio/clinvar_strict_rebuild_v1/01_raw_manifest/esm2_only_v1/core_embeddings/protein_mapping.tsv.gz`
|
| 14 |
+
- ESM array shape: `(14231, 640)`; valid rows: `14,231`; finite: `true`
|
| 15 |
+
- Split source: `/root/autodl-tmp/bio/inductive_graph_residual_extension/split_design/PROPOSED_PROTEIN_SPLIT.tsv`
|
| 16 |
+
- Train/test counts: `11,385` / `2,846`; protein intersection: `0`
|
| 17 |
+
- No corpus-level normalization, vocabulary, or feature fitting uses test proteins.
|
| 18 |
+
|
| 19 |
+
## Explicit exclusions
|
| 20 |
+
|
| 21 |
+
The graph workspace contains disease, PTM, pathway, and other graph-linked
|
| 22 |
+
annotations. They are excluded even where precomputed coverage exists. GO,
|
| 23 |
+
disease, PTM, pathway, target labels, PPI/task edges, graph statistics, and all
|
| 24 |
+
protein-ID/node-index lookup embeddings are forbidden by the YAML contract.
|
| 25 |
+
Feature availability by itself is not evidence that a feature is target-blind.
|
| 26 |
+
|
| 27 |
+
The ESM embedding is accepted here as a frozen sequence-derived representation
|
| 28 |
+
whose rows are aligned to the protein mapping. The contract does not permit
|
| 29 |
+
using an embedding table keyed by protein ID at inference time.
|
| 30 |
+
|
| 31 |
+
## Scope limitation
|
| 32 |
+
|
| 33 |
+
This is a protein-ID-disjoint audit. It does not claim sequence-cluster or
|
| 34 |
+
homology-disjoint generalization. That stronger split should be a later,
|
| 35 |
+
separately audited design if required.
|
initial_data/inductive_graph_residual_extension/audits/INDUCTIVE_GRAPH_SPLIT_AUDIT.md
ADDED
|
@@ -0,0 +1,30 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# Inductive graph split audit
|
| 2 |
+
|
| 3 |
+
## Roles
|
| 4 |
+
|
| 5 |
+
- Source graph: `/root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core` (read-only).
|
| 6 |
+
- `G_train`: 11,385 train proteins; all source edges incident to test proteins are removed from this view.
|
| 7 |
+
- `G_test_context`: 2,846 test proteins and held-out incident-edge references only; `train_eligible: false`.
|
| 8 |
+
- `G_test_context` must not be loaded by a training dataloader. It exists only to audit what neighbors are available at inference.
|
| 9 |
+
- Split source: `/root/autodl-tmp/bio/inductive_graph_residual_extension/split_design/PROPOSED_PROTEIN_SPLIT.tsv`.
|
| 10 |
+
|
| 11 |
+
## Required checks
|
| 12 |
+
|
| 13 |
+
- `train_test_node_overlap = 0` (protein IDs; train and test sets are disjoint).
|
| 14 |
+
- `train_test_edge_overlap = 0` (canonical source relation plus original `(src_index, dst_index)` tuples).
|
| 15 |
+
- The original graph core and its edge files were not modified.
|
| 16 |
+
|
| 17 |
+
## Edge counts
|
| 18 |
+
|
| 19 |
+
| relation file | G_train edges | G_test_context edges | source edges |
|
| 20 |
+
|---|---:|---:|---:|
|
| 21 |
+
| `disease__has_mutation__mutation.tsv.gz` | 1,300,380 | 0 | 1,300,380 |
|
| 22 |
+
| `disease__has_protein__protein.tsv.gz` | 230,965 | 57,411 | 288,376 |
|
| 23 |
+
| `disease__has_ptm__ptm.tsv.gz` | 298,704 | 0 | 298,704 |
|
| 24 |
+
| `mutation__on_protein__protein.tsv.gz` | 858,478 | 197,343 | 1,055,821 |
|
| 25 |
+
| `protein__has_ptm__ptm.tsv.gz` | 132,450 | 33,838 | 166,288 |
|
| 26 |
+
| `protein__in_pathway__pathway.tsv.gz` | 94,516 | 24,739 | 119,255 |
|
| 27 |
+
|
| 28 |
+
## Interpretation
|
| 29 |
+
|
| 30 |
+
The strict train-graph view gives an unseen protein no graph incident edge during training. The context view separately records held-out source-graph neighbors for inference-availability auditing. This construction is deliberately stronger than allowing a test protein's edges to remain in a shared graph, and it does not claim that test neighbors are usable during training.
|
initial_data/inductive_graph_residual_extension/audits/PHASE1_STATUS.tsv
ADDED
|
@@ -0,0 +1,9 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
check status value evidence
|
| 2 |
+
feature_contract PASS LOCKED contracts/INDUCTIVE_FEATURE_CONTRACT.yaml
|
| 3 |
+
feature_leakage PASS sequence-derived only audits/FEATURE_LEAKAGE_AUDIT.md
|
| 4 |
+
protein_universe PASS 14231 graph_core/node_mappings/protein.tsv
|
| 5 |
+
train_test_node_overlap PASS 0 audits/INDUCTIVE_GRAPH_SPLIT_AUDIT.md
|
| 6 |
+
train_test_edge_overlap PASS 0 audits/INDUCTIVE_GRAPH_SPLIT_AUDIT.md
|
| 7 |
+
encoder_static_shape PASS (4, 64) audits/ENCODER_STATIC_SHAPE_TEST.md
|
| 8 |
+
old_model_modified PASS NO Phase 1 writes only below inductive_graph_residual_extension
|
| 9 |
+
training PASS NO static forward test only
|
initial_data/inductive_graph_residual_extension/contracts/INDUCTIVE_FEATURE_CONTRACT.yaml
ADDED
|
@@ -0,0 +1,47 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version: 1
|
| 2 |
+
status: LOCKED
|
| 3 |
+
target_blind: true
|
| 4 |
+
split_protocol: protein_disjoint
|
| 5 |
+
training_status: not_started
|
| 6 |
+
|
| 7 |
+
allowed_features:
|
| 8 |
+
- name: esm2_embedding
|
| 9 |
+
dimension: 640
|
| 10 |
+
dtype: float32
|
| 11 |
+
source: frozen ESM2 protein-sequence embedding
|
| 12 |
+
derivation: protein sequence only; no split-fitted statistics
|
| 13 |
+
available_for_unseen_node: true
|
| 14 |
+
source_asset: /root/autodl-tmp/bio/clinvar_strict_rebuild_v1/01_raw_manifest/esm2_only_v1/core_embeddings/protein_esm2_embeddings.npy
|
| 15 |
+
- name: protein_length
|
| 16 |
+
dimension: 1
|
| 17 |
+
dtype: float32
|
| 18 |
+
source: protein sequence
|
| 19 |
+
derivation: sequence length, computed independently per protein
|
| 20 |
+
available_for_unseen_node: true
|
| 21 |
+
- name: amino_acid_composition
|
| 22 |
+
dimension: 20
|
| 23 |
+
dtype: float32
|
| 24 |
+
source: protein sequence
|
| 25 |
+
derivation: normalized counts over the 20 canonical amino acids
|
| 26 |
+
available_for_unseen_node: true
|
| 27 |
+
|
| 28 |
+
feature_vector:
|
| 29 |
+
order: [esm2_embedding, protein_length, amino_acid_composition]
|
| 30 |
+
dimension: 661
|
| 31 |
+
normalization: no corpus-level fit; any fixed transform must be declared in a later revision
|
| 32 |
+
|
| 33 |
+
forbidden_features:
|
| 34 |
+
- protein_id_or_node_index_lookup
|
| 35 |
+
- GO
|
| 36 |
+
- disease
|
| 37 |
+
- PTM
|
| 38 |
+
- pathway
|
| 39 |
+
- target_labels_or_benchmark_labels
|
| 40 |
+
- PPI_or_task_edges
|
| 41 |
+
- graph_statistics
|
| 42 |
+
|
| 43 |
+
leakage_rule: >-
|
| 44 |
+
A feature is admissible only when it can be computed from the held-out
|
| 45 |
+
protein sequence without reading target labels, task edges, split-fitted
|
| 46 |
+
statistics, or a protein-ID embedding table. Existing availability does not
|
| 47 |
+
override this contract.
|
initial_data/inductive_graph_residual_extension/datasets/G_test_context/CONTEXT_ONLY.txt
ADDED
|
@@ -0,0 +1,2 @@
|
|
|
|
|
|
|
|
|
|
| 1 |
+
This is held-out adjacency context only. It is not a training graph and must not be loaded by a training dataloader.
|
| 2 |
+
Protein node_index values are context-local; neighbor references retain original graph indices.
|
initial_data/inductive_graph_residual_extension/datasets/G_test_context/graph_manifest.json
ADDED
|
@@ -0,0 +1,16 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"role": "G_test_context",
|
| 3 |
+
"train_eligible": false,
|
| 4 |
+
"test_context": true,
|
| 5 |
+
"protein_nodes": 2846,
|
| 6 |
+
"neighbor_refs": 313331,
|
| 7 |
+
"edge_counts": {
|
| 8 |
+
"disease__has_protein__protein.tsv.gz": 57411,
|
| 9 |
+
"mutation__on_protein__protein.tsv.gz": 197343,
|
| 10 |
+
"protein__has_ptm__ptm.tsv.gz": 33838,
|
| 11 |
+
"protein__in_pathway__pathway.tsv.gz": 24739
|
| 12 |
+
},
|
| 13 |
+
"source_graph": "/root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core",
|
| 14 |
+
"source_graph_unchanged": true,
|
| 15 |
+
"note": "held-out test-protein incident edges only; neighbor indices are references to source graph mappings"
|
| 16 |
+
}
|
initial_data/inductive_graph_residual_extension/datasets/G_test_context/node_mappings/protein.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
initial_data/inductive_graph_residual_extension/datasets/G_train/graph_manifest.json
ADDED
|
@@ -0,0 +1,18 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"role": "G_train",
|
| 3 |
+
"train_eligible": true,
|
| 4 |
+
"test_context": false,
|
| 5 |
+
"protein_nodes": 11385,
|
| 6 |
+
"all_source_node_mappings_except_protein": true,
|
| 7 |
+
"test_protein_incident_edges_present": false,
|
| 8 |
+
"edge_counts": {
|
| 9 |
+
"disease__has_mutation__mutation.tsv.gz": 1300380,
|
| 10 |
+
"disease__has_protein__protein.tsv.gz": 230965,
|
| 11 |
+
"disease__has_ptm__ptm.tsv.gz": 298704,
|
| 12 |
+
"mutation__on_protein__protein.tsv.gz": 858478,
|
| 13 |
+
"protein__has_ptm__ptm.tsv.gz": 132450,
|
| 14 |
+
"protein__in_pathway__pathway.tsv.gz": 94516
|
| 15 |
+
},
|
| 16 |
+
"source_graph": "/root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core",
|
| 17 |
+
"source_graph_unchanged": true
|
| 18 |
+
}
|
initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/disease.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/pathway.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
initial_data/inductive_graph_residual_extension/datasets/G_train/node_mappings/protein.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
initial_data/inductive_graph_residual_extension/datasets/G_train/relation_mappings.tsv
ADDED
|
@@ -0,0 +1,13 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
relation_index relation src_type dst_type direction
|
| 2 |
+
0 mutation__on_protein__protein mutation protein forward
|
| 3 |
+
1 protein__rev_on_protein__mutation protein mutation reverse
|
| 4 |
+
2 protein__has_ptm__ptm protein ptm forward
|
| 5 |
+
3 ptm__rev_has_ptm__protein ptm protein reverse
|
| 6 |
+
4 protein__in_pathway__pathway protein pathway forward
|
| 7 |
+
5 pathway__rev_in_pathway__protein pathway protein reverse
|
| 8 |
+
6 disease__has_mutation__mutation disease mutation forward
|
| 9 |
+
7 mutation__rev_has_mutation__disease mutation disease reverse
|
| 10 |
+
8 disease__has_ptm__ptm disease ptm forward
|
| 11 |
+
9 ptm__rev_has_ptm__disease ptm disease reverse
|
| 12 |
+
10 disease__has_protein__protein disease protein forward
|
| 13 |
+
11 protein__rev_has_protein__disease protein disease reverse
|
initial_data/inductive_graph_residual_extension/datasets/INDUCTIVE_SPLIT.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
initial_data/inductive_graph_residual_extension/feature_inventory/PROTEIN_FEATURE_INVENTORY.tsv
ADDED
|
@@ -0,0 +1,12 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
feature dimension source coverage available_for_unseen_node leakage_risk
|
| 2 |
+
ESM2 embedding 640 /root/autodl-tmp/bio/clinvar_strict_rebuild_v1/01_raw_manifest/esm2_only_v1/core_embeddings/protein_esm2_embeddings.npy; explicit protein_mapping.tsv.gz 14231/14231 (100.00%) YES if recomputed from sequence; archived row is not an inductive graph feature LOW-MEDIUM: frozen sequence model; check temporal/homology policy
|
| 3 |
+
raw amino-acid sequence variable length /root/autodl-tmp/bio/UP000005640_9606.fasta; UniProt raw sequence assets 14218/14231 FASTA rows; ESM valid 14231/14231 YES, subject to sequence retrieval LOW for sequence-only input; pretraining overlap must be disclosed
|
| 4 |
+
protein length 1 /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/node_mappings/protein.tsv; sequence_length 14231/14231 (100.00%) YES, derived from sequence LOW
|
| 5 |
+
amino-acid composition 20 (recommended; optionally 21 incl. X) derivable from raw sequence; not materialized in current V2 14218/14231 direct FASTA derivation YES, after deterministic sequence featurization LOW
|
| 6 |
+
gene symbol / protein name categorical/text metadata /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/node_mappings/protein.tsv 14231/14231 gene symbols; 14231/14231 names CONDITIONAL on UniProt annotation lookup LOW-MEDIUM
|
| 7 |
+
domain annotation variable sparse set; UniProt FT DOMAIN /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_raw/uniprot/uniprot_sprot_human.dat.gz; GFF companion: /root/autodl-tmp/bio/idmapping_model_organism_9606_2026_05_24.gff 6792/14231 graph proteins in UniProt DAT CONDITIONAL on external annotation availability MEDIUM: curated functional annotation; must be frozen before evaluation
|
| 8 |
+
GO annotation 398D current gate vocabulary (102 MF + 166 BP + 130 CC); raw set is variable /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_raw/uniprot/uniprot_sprot_human.dat.gz; vocabulary /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/26_go_ec_gate/protocols/go_term_vocabulary.tsv 13986/14231 (98.28%) CONDITIONAL on annotation availability; vocabulary must be train-only HIGH: functional labels can overlap PPI/benchmark semantics
|
| 9 |
+
PTM site annotation variable sparse set; UniProt MOD_RES and PTM graph neighbors /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_raw/uniprot/uniprot_sprot_human.dat.gz; /root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_processed_core/nodes_ptm.tsv; protein__has_ptm__ptm 8798/14231 DAT MOD_RES; graph PTM adjacency 14231/14231 CONDITIONAL on independent PTM database at inference HIGH for PTM-related tasks; graph context can be target-proximal
|
| 10 |
+
Reactome pathway membership 2791 pathway IDs (sparse multi-hot) /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/node_mappings/pathway.tsv; protein__in_pathway__pathway; Reactome 9080/14231 (63.83%) CONDITIONAL on pathway annotation availability MEDIUM-HIGH: existing graph relation; freeze and exclude target-derived edges
|
| 11 |
+
disease association 19019 disease IDs (sparse multi-hot) /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/edges/disease__has_protein__protein.tsv.gz; ClinVar_UniProt mapping 14231/14231 (100.00%) CONDITIONAL; not safe unless independently known at inference HIGH: ClinVar/disease associations are target-proximal
|
| 12 |
+
graph statistics 4 relation-specific degrees (mutation/PTM/pathway/disease); optional log1p /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/edges; derived only from incident edges 14231/14231 have at least one core relation CONDITIONAL on inference-time relations; no current V2 encoder HIGH unless every target-derived relation is excluded
|
initial_data/inductive_graph_residual_extension/inductive_phase2_small/data/FEATURE_SOURCE_MANIFEST.json
ADDED
|
@@ -0,0 +1,24 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"feature_dimension": 661,
|
| 3 |
+
"esm2_dimension": 640,
|
| 4 |
+
"sequence_rows_primary": 14218,
|
| 5 |
+
"dat_fallback_rows": 13,
|
| 6 |
+
"sequence_coverage": 14231,
|
| 7 |
+
"esm_rows": 14231,
|
| 8 |
+
"esm_dtype_source": "float16",
|
| 9 |
+
"feature_dtype": "float32",
|
| 10 |
+
"length_transform": "sequence_length / 1000.0 (fixed, not fit)",
|
| 11 |
+
"aa_composition": "20 canonical amino-acid counts / sequence length",
|
| 12 |
+
"forbidden_feature_sources_read": [
|
| 13 |
+
"GO",
|
| 14 |
+
"PTM",
|
| 15 |
+
"disease",
|
| 16 |
+
"pathway",
|
| 17 |
+
"graph_statistics"
|
| 18 |
+
],
|
| 19 |
+
"source_files": [
|
| 20 |
+
"/root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/28_ppi_gate/source_esm_protocol/assets/protein_sequences.tsv.gz",
|
| 21 |
+
"/root/autodl-tmp/bio/disease_mutation_ptm_gcl/data_raw/uniprot/uniprot_sprot_human.dat.gz",
|
| 22 |
+
"/root/autodl-tmp/bio/clinvar_strict_rebuild_v1/01_raw_manifest/esm2_only_v1/core_embeddings/protein_esm2_embeddings.npy"
|
| 23 |
+
]
|
| 24 |
+
}
|
initial_data/inductive_graph_residual_extension/inductive_phase2_small/data/PPI_SOURCE_MANIFEST.json
ADDED
|
@@ -0,0 +1,11 @@
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"source_rows": 60438,
|
| 3 |
+
"covered_rows": 60438,
|
| 4 |
+
"train_graph_edges": 35396,
|
| 5 |
+
"validation_edges": 3948,
|
| 6 |
+
"test_edges": 21094,
|
| 7 |
+
"train_graph_nodes": 7508,
|
| 8 |
+
"test_query_proteins": 2041,
|
| 9 |
+
"source_sha256": "778ee1f24221d640d9b724b804960c3d6efef0b7483afe0398b499dba2224db6",
|
| 10 |
+
"source": "/root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/28_ppi_gate/source_esm_protocol/assets/positive_physical_ppi.tsv.gz"
|
| 11 |
+
}
|
initial_data/inductive_graph_residual_extension/inductive_phase2_small/data/protein_feature_index.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
initial_data/inductive_graph_residual_extension/phase3a_link_split_audit/audits/INDUCTIVE_EDGE_CONTEXT_STATISTICS.tsv
ADDED
|
@@ -0,0 +1,21 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
scope metric value definition evidence
|
| 2 |
+
source protein_universe 14231 canonical graph mapping universe /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/graph_core/node_mappings/protein.tsv
|
| 3 |
+
source source_edges 60438 deduplicated canonical undirected PPI pairs /root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/28_ppi_gate/source_esm_protocol/assets/positive_physical_ppi.tsv.gz
|
| 4 |
+
split train_edges 48350 all source edges not selected for test holdout /root/autodl-tmp/bio/inductive_graph_residual_extension/phase3a_link_split_audit/datasets/INDUCTIVE_LINK_TRAIN_EDGES.tsv.gz
|
| 5 |
+
split test_edges 12088 deterministic edge holdout /root/autodl-tmp/bio/inductive_graph_residual_extension/phase3a_link_split_audit/datasets/INDUCTIVE_LINK_TEST_EDGES.tsv.gz
|
| 6 |
+
split test_edge_fraction 0.200006618352692 test_edges/source_edges phase3a_deterministic_edge_holdout_v1
|
| 7 |
+
test_queries query_count 5803 unique endpoints of test edges /root/autodl-tmp/bio/inductive_graph_residual_extension/phase3a_link_split_audit/datasets/INDUCTIVE_LINK_TEST_EDGES.tsv.gz
|
| 8 |
+
test_queries candidate_count 14230 existing evaluator all-protein candidates minus self /root/autodl-tmp/bio/inductive_graph_residual_extension/inductive_phase2_small/logs/phase2_small_train.py:retrieval_metrics
|
| 9 |
+
test_queries train_degree_mean 14.870584180596243 training graph degree among test query proteins phase3a_deterministic_edge_holdout_v1
|
| 10 |
+
test_queries train_degree_median 7 training graph degree among test query proteins phase3a_deterministic_edge_holdout_v1
|
| 11 |
+
test_queries train_degree_p90 32.0 training graph degree among test query proteins phase3a_deterministic_edge_holdout_v1
|
| 12 |
+
test_queries train_degree_zero_count 0 query proteins with no training incident edge phase3a_deterministic_edge_holdout_v1
|
| 13 |
+
test_queries train_degree_zero_fraction 0.0 zero-degree query count/query count phase3a_deterministic_edge_holdout_v1
|
| 14 |
+
test_queries query_nodes_present_in_train_graph 5803 test query proteins with at least one training edge phase3a_deterministic_edge_holdout_v1
|
| 15 |
+
leakage direct_edge_overlap 0 canonical E_train intersection E_test canonical sorted node pairs
|
| 16 |
+
leakage reverse_edge_overlap 0 raw-direction reverse duplicates across split canonical sorted node pairs
|
| 17 |
+
leakage duplicate_pair_train 0 duplicate canonical pairs in train split set cardinality check
|
| 18 |
+
leakage duplicate_pair_test 0 duplicate canonical pairs in test split set cardinality check
|
| 19 |
+
leakage alias_overlap 0 non-canonical/unmapped source ID tokens protein.tsv canonical node_id check
|
| 20 |
+
availability temporal_metadata_available FALSE source contains date/timestamp/release field protein_a,protein_b,nbexp_max,nbexp_sum,annotation_count,intact_ids
|
| 21 |
+
availability test_query_neighbor_available YES every test query has a training graph neighbor phase3a_deterministic_edge_holdout_v1
|
initial_data/inductive_graph_residual_extension/phase3a_link_split_audit/audits/INDUCTIVE_LINK_LEAKAGE_AUDIT.tsv
ADDED
|
@@ -0,0 +1,7 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
check value status evidence
|
| 2 |
+
direct_edge_overlap 0 PASS canonical sorted undirected pair
|
| 3 |
+
reverse_edge_overlap 0 PASS raw source ID direction cross-check
|
| 4 |
+
duplicate_pair_train 0 PASS train set cardinality
|
| 5 |
+
duplicate_pair_test 0 PASS test set cardinality
|
| 6 |
+
alias_overlap 0 PASS all source IDs exact-match canonical UniProt mapping
|
| 7 |
+
test_query_zero_degree 0 PASS train degree after holdout
|
initial_data/inductive_graph_residual_extension/phase3a_link_split_audit/logs/PHASE3A_LINK_SPLIT_AUDIT.json
ADDED
|
@@ -0,0 +1,30 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"phase": "Inductive Graph-Residual Phase 3A",
|
| 3 |
+
"audit_only": true,
|
| 4 |
+
"training_started": false,
|
| 5 |
+
"split_version": "phase3a_deterministic_edge_holdout_v1",
|
| 6 |
+
"valid_split": true,
|
| 7 |
+
"node_split": false,
|
| 8 |
+
"protein_universe": 14231,
|
| 9 |
+
"source": "/root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/28_ppi_gate/source_esm_protocol/assets/positive_physical_ppi.tsv.gz",
|
| 10 |
+
"source_sha256": "778ee1f24221d640d9b724b804960c3d6efef0b7483afe0398b499dba2224db6",
|
| 11 |
+
"train_edges": 48350,
|
| 12 |
+
"test_edges": 12088,
|
| 13 |
+
"test_queries": 5803,
|
| 14 |
+
"candidate_count": 14230,
|
| 15 |
+
"train_degree_mean_test_queries": 14.870584180596243,
|
| 16 |
+
"train_degree_median_test_queries": 7,
|
| 17 |
+
"test_query_zero_degree_count": 0,
|
| 18 |
+
"test_query_zero_degree_fraction": 0.0,
|
| 19 |
+
"query_nodes_in_train_graph": 5803,
|
| 20 |
+
"leakage": {
|
| 21 |
+
"direct_edge_overlap": 0,
|
| 22 |
+
"reverse_edge_overlap": 0,
|
| 23 |
+
"duplicate_pair_train": 0,
|
| 24 |
+
"duplicate_pair_test": 0,
|
| 25 |
+
"alias_overlap": 0
|
| 26 |
+
},
|
| 27 |
+
"temporal_metadata_available": false,
|
| 28 |
+
"next_step": "TRAIN_INDUCTIVE_GR",
|
| 29 |
+
"report": "/root/autodl-tmp/bio/inductive_graph_residual_extension/phase3a_link_split_audit/reports/INDUCTIVE_LINK_SPLIT_FEASIBILITY.md"
|
| 30 |
+
}
|
initial_data/inductive_graph_residual_extension/phase3a_link_split_audit/reports/INDUCTIVE_LINK_SPLIT_FEASIBILITY.md
ADDED
|
@@ -0,0 +1,92 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# Inductive link split feasibility
|
| 2 |
+
|
| 3 |
+
## Decision
|
| 4 |
+
|
| 5 |
+
`VALID SPLIT: YES` for a link-level inductive evaluation candidate.
|
| 6 |
+
|
| 7 |
+
The split is **edge-holdout**, not node-disjoint: proteins may occur in both
|
| 8 |
+
the training graph and the test-edge endpoint/query set. Every endpoint of a
|
| 9 |
+
held-out test edge retains at least one incident training edge, so the test
|
| 10 |
+
query has an available training-graph neighborhood.
|
| 11 |
+
|
| 12 |
+
## Construction
|
| 13 |
+
|
| 14 |
+
- Protein universe: `14,231` canonical graph nodes.
|
| 15 |
+
- Source: `/root/autodl-tmp/bio/disease_mutation_ptm_gcl/work/amplify_generalization/28_ppi_gate/source_esm_protocol/assets/positive_physical_ppi.tsv.gz`.
|
| 16 |
+
- Source SHA256: `778ee1f24221d640d9b724b804960c3d6efef0b7483afe0398b499dba2224db6`.
|
| 17 |
+
- Source edges: `60,438` unique undirected canonical pairs.
|
| 18 |
+
- Temporal metadata: **not available** in the source schema
|
| 19 |
+
(`protein_a, protein_b, nbexp_max, nbexp_sum, annotation_count, intact_ids`); therefore no temporal claim is
|
| 20 |
+
made.
|
| 21 |
+
- Proposal: `phase3a_deterministic_edge_holdout_v1`; deterministic SHA-256 edge ranking, target
|
| 22 |
+
holdout fraction `20%`.
|
| 23 |
+
- Train edges: `48,350`.
|
| 24 |
+
- Test edges: `12,088`.
|
| 25 |
+
- Test query proteins: `5,803` unique test-edge endpoints.
|
| 26 |
+
|
| 27 |
+
The selection only considers edges whose two source degrees are at least two
|
| 28 |
+
and enforces a per-node holdout cap of `source_degree - 1`. This is why the
|
| 29 |
+
result has zero-degree query fraction `0/5,803 = 0.000000` while
|
| 30 |
+
retaining test proteins in the training graph.
|
| 31 |
+
|
| 32 |
+
## Neighbor availability
|
| 33 |
+
|
| 34 |
+
| quantity | value |
|
| 35 |
+
|---|---:|
|
| 36 |
+
| test query count | 5,803 |
|
| 37 |
+
| average training degree | 14.870584 |
|
| 38 |
+
| median training degree | 7.000000 |
|
| 39 |
+
| p90 training degree | 32.000000 |
|
| 40 |
+
| zero-degree test queries | 0 |
|
| 41 |
+
| zero-degree fraction | 0.000000% |
|
| 42 |
+
| query proteins present in training graph | 5,803/5,803 |
|
| 43 |
+
|
| 44 |
+
## Leakage audit
|
| 45 |
+
|
| 46 |
+
All required checks are zero:
|
| 47 |
+
|
| 48 |
+
| check | value | status |
|
| 49 |
+
|---|---:|---|
|
| 50 |
+
| direct canonical edge overlap | 0 | PASS |
|
| 51 |
+
| reverse edge overlap | 0 | PASS |
|
| 52 |
+
| duplicate train pair | 0 | PASS |
|
| 53 |
+
| duplicate test pair | 0 | PASS |
|
| 54 |
+
| alias/non-canonical ID overlap | 0 | PASS |
|
| 55 |
+
|
| 56 |
+
The source has one canonical `uniprot_id` per `PROT:<uniprot_id>` node and no
|
| 57 |
+
alias namespace in the PPI file. All source endpoint IDs exact-match this
|
| 58 |
+
mapping; the alias check therefore reports zero unresolved or alternate IDs.
|
| 59 |
+
|
| 60 |
+
## Candidate pool and evaluator contract
|
| 61 |
+
|
| 62 |
+
The existing PPI retrieval convention is retained:
|
| 63 |
+
|
| 64 |
+
- positive definition: undirected held-out PPI test edges;
|
| 65 |
+
- query cohort: unique endpoints of the held-out test edges;
|
| 66 |
+
- candidate universe: all `14,231` protein rows;
|
| 67 |
+
- self-exclusion: candidate count `14,230` per query;
|
| 68 |
+
- scoring/rank definitions: unchanged from
|
| 69 |
+
`/root/autodl-tmp/bio/inductive_graph_residual_extension/inductive_phase2_small/logs/phase2_small_train.py:773-806`.
|
| 70 |
+
|
| 71 |
+
This audit does not run retrieval and does not alter the existing evaluator.
|
| 72 |
+
|
| 73 |
+
## Answers
|
| 74 |
+
|
| 75 |
+
1. **是否存在合法 inductive link split？** Yes, as an edge-level holdout
|
| 76 |
+
candidate with nonempty training context for every test query.
|
| 77 |
+
2. **test query 数量？** `5,803`.
|
| 78 |
+
3. **平均训练邻居？** `14.870584`.
|
| 79 |
+
4. **是否适合 GraphResidual inductive encoder？** Yes for a controlled pilot:
|
| 80 |
+
the encoder can receive sequence features plus training-graph neighbors for
|
| 81 |
+
every test query, while test edges are held out from context.
|
| 82 |
+
5. **是否值得进入正式训练？** Yes, but only after freezing this split and
|
| 83 |
+
evaluator contract; this Phase 3A audit itself performed no training.
|
| 84 |
+
|
| 85 |
+
## Files
|
| 86 |
+
|
| 87 |
+
- `datasets/INDUCTIVE_LINK_TRAIN_EDGES.tsv.gz`
|
| 88 |
+
- `datasets/INDUCTIVE_LINK_TEST_EDGES.tsv.gz`
|
| 89 |
+
- `audits/INDUCTIVE_EDGE_CONTEXT_STATISTICS.tsv`
|
| 90 |
+
- `audits/INDUCTIVE_LINK_LEAKAGE_AUDIT.tsv`
|
| 91 |
+
|
| 92 |
+
`NEXT STEP: TRAIN_INDUCTIVE_GR` under this newly locked link-level protocol.
|
initial_data/inductive_graph_residual_extension/reports/CLAIM_BOUNDARY.md
ADDED
|
@@ -0,0 +1,27 @@
|
|
|
|
|
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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 |
+
# CLAIM BOUNDARY
|
| 2 |
+
|
| 3 |
+
## Original Graph-Residual V2
|
| 4 |
+
|
| 5 |
+
The original method is **transductive and lookup-based on the graph side**. A learned 64D graph embedding is stored per node and aligned through a fixed node-ID/index mapping. Graph-Residual V2 applies a learned `64 -> 256 -> 640` residual projector and fuses it with ESM2. It does not construct a graph representation for a protein that lacks a precomputed graph row.
|
| 6 |
+
|
| 7 |
+
## Proposed extension
|
| 8 |
+
|
| 9 |
+
The proposed method is **inductive and encoder-based**. It would compute a 64D graph representation from node features, neighbor features, and relation types at inference time, then reuse the existing residual interface where compatible.
|
| 10 |
+
|
| 11 |
+
## Non-equivalence statement
|
| 12 |
+
|
| 13 |
+
The two are **not the same model**. The proposed extension changes the graph representation function and its train/test information contract; it cannot inherit the original V2's transductive graph lookup claim. Original V2 results remain valid only under their original transductive input contract. Any result on the proposed protein-disjoint split must be labeled as an inductive-extension result and must not be reported as an evaluation of the original V2.
|
| 14 |
+
|
| 15 |
+
## What Phase 0 establishes
|
| 16 |
+
|
| 17 |
+
- `V_train ∩ V_test = empty` for the proposed 80/20 protein split.
|
| 18 |
+
- Sequence-derived input is available for all proposed test proteins in the archived ESM2 validity mask.
|
| 19 |
+
- Full source graph relations are present for the test proteins, but their incident edges are removed from the strict training graph and can be exposed only in a declared inference-time context regime.
|
| 20 |
+
- The current V2 path has no unseen-node generation function, message passing, or graph-missing branch.
|
| 21 |
+
|
| 22 |
+
## What Phase 0 does not establish
|
| 23 |
+
|
| 24 |
+
- It does not establish that the new encoder will improve PPI retrieval.
|
| 25 |
+
- It does not validate a new checkpoint or a new benchmark.
|
| 26 |
+
- It does not establish sequence-cluster disjointness; the proposal is protein-ID disjoint only.
|
| 27 |
+
- It does not license using GO/PTM/disease/pathway annotations without a separate leakage and availability lock.
|
initial_data/inductive_graph_residual_extension/reports/INDUCTIVE_EXPERIMENT_PLAN.md
ADDED
|
@@ -0,0 +1,46 @@
|
|
|
|
|
|
|
|
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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 |
+
# INDUCTIVE EXPERIMENT PLAN
|
| 2 |
+
|
| 3 |
+
Status: design only; no training or evaluation was started in Phase 0.
|
| 4 |
+
|
| 5 |
+
## Primary task
|
| 6 |
+
|
| 7 |
+
Priority task: **PPI retrieval** on a protein-level disjoint split. The PPI target relation must be held out from all encoder inputs. The current core graph has no direct PPI relation, which is compatible with a target-blind protocol, but all other graph relations used as context must be frozen and audited before scoring.
|
| 8 |
+
|
| 9 |
+
## Baselines and methods
|
| 10 |
+
|
| 11 |
+
1. **ESM2**: frozen sequence-only representation; valid for unseen proteins with a sequence.
|
| 12 |
+
2. **Original Graph-Residual**: transductive lookup-based reference. It may be reported as an original-method reference/oracle only when its fixed graph rows are available; it is not a valid strict-inductive baseline for a test protein absent from the graph table.
|
| 13 |
+
3. **Inductive Graph-Residual**: new feature-based, relation-aware encoder producing 64D graph representations, followed by the existing residual interface where dimensionally and contractually compatible.
|
| 14 |
+
|
| 15 |
+
The comparison must state the information regime for each method. No original V2 checkpoint may be modified to make it appear inductive.
|
| 16 |
+
|
| 17 |
+
## Split and information lock
|
| 18 |
+
|
| 19 |
+
- Protein-level split: 80/20 over the current 14,231-protein universe, deterministic SHA256 assignment, `V_train ∩ V_test = empty`.
|
| 20 |
+
- Remove test proteins and all incident training edges before fitting the inductive encoder.
|
| 21 |
+
- At inference, declare one of: sequence-only; sequence plus permitted held-out neighbors; or no-information. Do not silently use a full-graph lookup row for a test protein.
|
| 22 |
+
- Keep the PPI target relation and any target-derived labels out of node features, neighbor features, graph statistics, and encoder training.
|
| 23 |
+
- Before formal use, add a secondary sequence-cluster-disjoint audit if the scientific claim is intended to be stronger than protein-ID disjointness.
|
| 24 |
+
|
| 25 |
+
## Metrics
|
| 26 |
+
|
| 27 |
+
Report per-query and aggregate:
|
| 28 |
+
|
| 29 |
+
- MRR
|
| 30 |
+
- Hits@10
|
| 31 |
+
- Hits@50
|
| 32 |
+
- Hits@100
|
| 33 |
+
|
| 34 |
+
Use the same candidate pool and query filtering across all three methods. Stratify or annotate results by graph-context availability and sequence similarity so sequence-only performance is not conflated with graph-context gains.
|
| 35 |
+
|
| 36 |
+
## Statistical design
|
| 37 |
+
|
| 38 |
+
- Seeds: **3** (`42`, `3407`, `2026`).
|
| 39 |
+
- Bootstrap replicates: **B = 5000**.
|
| 40 |
+
- Bootstrap unit: query protein (not individual candidate edge) for retrieval metrics; preserve query-level clustering.
|
| 41 |
+
- Report point estimate, bootstrap 95% interval, and paired method differences using the same queries/candidate pools.
|
| 42 |
+
- Lock preprocessing, split assignment, relation availability, and feature vocabulary before any model fitting.
|
| 43 |
+
|
| 44 |
+
## Stop conditions
|
| 45 |
+
|
| 46 |
+
Stop before training if any test protein receives a train-time graph row, if target PPI edges enter the encoder, if a feature is unavailable for the claimed unseen-node regime, or if the original V2 and inductive extension are not kept as separate model identities.
|
initial_data/inductive_graph_residual_extension/reports/INDUCTIVE_GR_INTERFACE.md
ADDED
|
@@ -0,0 +1,56 @@
|
|
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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 |
+
# Inductive Graph-Residual interface
|
| 2 |
+
|
| 3 |
+
## Existing Graph-Residual V2 boundary
|
| 4 |
+
|
| 5 |
+
```text
|
| 6 |
+
protein_id
|
| 7 |
+
-> fixed graph lookup embedding (64D)
|
| 8 |
+
-> existing residual adapter (64 -> 256 -> 640)
|
| 9 |
+
-> residual fusion with the ESM2 640D branch
|
| 10 |
+
```
|
| 11 |
+
|
| 12 |
+
The existing V2 model remains unchanged. Its graph representation is supplied
|
| 13 |
+
by the recovered lookup-based graph-pretraining path, not by neighbor
|
| 14 |
+
aggregation at model forward time.
|
| 15 |
+
|
| 16 |
+
## Phase 1 extension boundary
|
| 17 |
+
|
| 18 |
+
```text
|
| 19 |
+
node_features (661D)
|
| 20 |
+
+ neighbor_features (K x 661D)
|
| 21 |
+
+ relation_ids (K)
|
| 22 |
+
-> InductiveGraphEncoder
|
| 23 |
+
-> 64D graph representation
|
| 24 |
+
-> original residual adapter (64 -> 256 -> 640)
|
| 25 |
+
-> existing residual fusion
|
| 26 |
+
```
|
| 27 |
+
|
| 28 |
+
The encoder consumes feature tensors and typed neighbor features. It does not
|
| 29 |
+
accept a protein ID, node index, or node embedding table. The locked feature
|
| 30 |
+
vector is 640D ESM2 plus sequence length plus 20D amino-acid composition.
|
| 31 |
+
Relation IDs are represented as one-hot inputs to a linear relation transform;
|
| 32 |
+
they are not node-ID embeddings.
|
| 33 |
+
|
| 34 |
+
## What changes
|
| 35 |
+
|
| 36 |
+
- Add a new inductive graph encoder module with a node feature encoder,
|
| 37 |
+
neighbor feature encoder, relation transform, masked mean message aggregate,
|
| 38 |
+
and a 64D output head.
|
| 39 |
+
- Add a data loader that constructs feature tensors from sequence-derived
|
| 40 |
+
inputs and uses only the permitted graph context at inference.
|
| 41 |
+
- Add a strict protein-disjoint split and keep `G_test_context` out of the
|
| 42 |
+
training input path.
|
| 43 |
+
|
| 44 |
+
## What remains unchanged
|
| 45 |
+
|
| 46 |
+
- The original Graph-Residual V2 source, checkpoint, benchmark, and paper are
|
| 47 |
+
not modified by Phase 1.
|
| 48 |
+
- The existing 64 -> 256 -> 640 residual adapter and the residual-fusion
|
| 49 |
+
concept remain the downstream interface.
|
| 50 |
+
- The ESM2 branch remains 640D. The new 64D graph vector is only a replacement
|
| 51 |
+
for the graph-representation provider when the extension is explicitly
|
| 52 |
+
implemented and trained.
|
| 53 |
+
|
| 54 |
+
This is an interface design and skeleton, not a claim that the original model
|
| 55 |
+
has become inductive through configuration alone. The old and new models must
|
| 56 |
+
be reported as distinct model variants.
|
initial_data/inductive_graph_residual_extension/reports/PHASE0_RESULT.md
ADDED
|
@@ -0,0 +1,29 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# INDUCTIVE GR PHASE 0 RESULT
|
| 2 |
+
|
| 3 |
+
CURRENT MODEL: **LOOKUP_BASED**
|
| 4 |
+
|
| 5 |
+
INDUCTIVE EXTENSION FEASIBLE: **YES at architecture/data feasibility level; UNCERTAIN for empirical success**
|
| 6 |
+
|
| 7 |
+
AVAILABLE NODE FEATURES: Full proposed test-set coverage for sequence-derived inputs: archived ESM2 640D, raw sequence/length, and derivable amino-acid composition. Conditional external annotations include GO (13986/14231), UniProt domain annotations (6792/14231), PTM annotations, Reactome pathway membership (9080/14231), disease associations, and relation-specific graph statistics. The latter groups have medium-to-high leakage risk and require a target-blind availability lock.
|
| 8 |
+
|
| 9 |
+
PROPOSED TEST PROTEINS: **2846**
|
| 10 |
+
|
| 11 |
+
SEQUENCE AVAILABLE: **YES (2846/2846)**
|
| 12 |
+
|
| 13 |
+
GRAPH NEIGHBOR AVAILABLE: **YES in the held-out source graph (2846/2846); NO in the strict train-graph view by design**
|
| 14 |
+
|
| 15 |
+
NEW MODEL REQUIRED: **YES**
|
| 16 |
+
|
| 17 |
+
TRAINING STARTED: **NO**
|
| 18 |
+
|
| 19 |
+
NEXT STEP: **IMPLEMENT_ENCODER** only after the feature/neighbor contract and target-blind split are locked. Do not reuse the original V2 lookup row for unseen proteins.
|
| 20 |
+
|
| 21 |
+
REPORTS:
|
| 22 |
+
|
| 23 |
+
- `/root/autodl-tmp/bio/inductive_graph_residual_extension/audit/CURRENT_GR_V2_SPEC.md`
|
| 24 |
+
- `/root/autodl-tmp/bio/inductive_graph_residual_extension/feature_inventory/PROTEIN_FEATURE_INVENTORY.tsv`
|
| 25 |
+
- `/root/autodl-tmp/bio/inductive_graph_residual_extension/split_design/INDUCTIVE_SPLIT_PROPOSAL.tsv`
|
| 26 |
+
- `/root/autodl-tmp/bio/inductive_graph_residual_extension/audit/UNSEEN_NODE_CASES.tsv`
|
| 27 |
+
- `/root/autodl-tmp/bio/inductive_graph_residual_extension/architecture/INDUCTIVE_GR_DESIGN.md`
|
| 28 |
+
- `/root/autodl-tmp/bio/inductive_graph_residual_extension/reports/CLAIM_BOUNDARY.md`
|
| 29 |
+
- `/root/autodl-tmp/bio/inductive_graph_residual_extension/reports/INDUCTIVE_EXPERIMENT_PLAN.md`
|
initial_data/inductive_graph_residual_extension/reports/PHASE1_RESULT.md
ADDED
|
@@ -0,0 +1,34 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
# INDUCTIVE GR PHASE 1
|
| 2 |
+
|
| 3 |
+
- **FEATURE CONTRACT:** LOCKED
|
| 4 |
+
- **LEAKAGE:** PASS
|
| 5 |
+
- **TRAIN TEST NODE OVERLAP:** 0
|
| 6 |
+
- **TRAIN TEST EDGE OVERLAP:** 0
|
| 7 |
+
- **INDUCTIVE ENCODER:** SKELETON READY
|
| 8 |
+
- **OLD MODEL MODIFIED:** NO
|
| 9 |
+
- **TRAINING:** NO
|
| 10 |
+
- **NEXT STEP:** TRAIN_SMALL_SCALE
|
| 11 |
+
|
| 12 |
+
## Dataset contract
|
| 13 |
+
|
| 14 |
+
- Protein universe: `14,231`
|
| 15 |
+
- Proposed test proteins: `2,846`
|
| 16 |
+
- Sequence-derived features available: `YES` for all proteins
|
| 17 |
+
- Neighbor availability: `YES` in `G_test_context`; `NO` in strict `G_train` for test proteins
|
| 18 |
+
- `G_test_context` is context-only and forbidden in training.
|
| 19 |
+
|
| 20 |
+
## Deliverables
|
| 21 |
+
|
| 22 |
+
- `contracts/INDUCTIVE_FEATURE_CONTRACT.yaml`
|
| 23 |
+
- `datasets/INDUCTIVE_SPLIT.tsv`
|
| 24 |
+
- `datasets/G_train/`
|
| 25 |
+
- `datasets/G_test_context/`
|
| 26 |
+
- `encoder/inductive_graph_encoder.py`
|
| 27 |
+
- `audits/FEATURE_LEAKAGE_AUDIT.md`
|
| 28 |
+
- `audits/INDUCTIVE_GRAPH_SPLIT_AUDIT.md`
|
| 29 |
+
- `audits/ENCODER_STATIC_SHAPE_TEST.md`
|
| 30 |
+
- `reports/INDUCTIVE_GR_INTERFACE.md`
|
| 31 |
+
|
| 32 |
+
The result is an implementation contract and static skeleton only. No model
|
| 33 |
+
training, task evaluation, checkpoint generation, benchmark edit, or paper
|
| 34 |
+
edit was performed.
|
initial_data/inductive_graph_residual_extension/split_design/INDUCTIVE_SPLIT_PROPOSAL.tsv
ADDED
|
@@ -0,0 +1,4 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
split train proteins test proteins coverage available features
|
| 2 |
+
train 11385 0 11385/14231 (80.0014%) sequence; ESM2 640D; length; AA composition; graph context only for train nodes; no test-node rows
|
| 3 |
+
test 0 2846 2846/14231 (19.9986%) sequence; ESM2 640D; length; AA composition; inference-time neighbor features only if independently available; no V2 lookup row
|
| 4 |
+
overlap_check 11385 2846 intersection=0; union=14231/14231 deterministic SHA256 protein-ID hash; protein-level disjoint; no sequence-cluster disjointness claim
|
initial_data/inductive_graph_residual_extension/split_design/PROPOSED_PROTEIN_SPLIT.tsv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
initial_data/root/final_prodisease_v32_clinvar_dataset.metadata.json
ADDED
|
@@ -0,0 +1,51 @@
|
|
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| 1 |
+
{
|
| 2 |
+
"output_file": "/root/autodl-tmp/bio/final_prodisease_v32_clinvar_dataset.parquet",
|
| 3 |
+
"n_rows": 39729,
|
| 4 |
+
"embedding_dim": 320,
|
| 5 |
+
"label_distribution": {
|
| 6 |
+
"1": 19885,
|
| 7 |
+
"0": 19844
|
| 8 |
+
},
|
| 9 |
+
"site_type_distribution": {
|
| 10 |
+
"independent": 39729
|
| 11 |
+
},
|
| 12 |
+
"columns": [
|
| 13 |
+
"source",
|
| 14 |
+
"label_type",
|
| 15 |
+
"cancer_type",
|
| 16 |
+
"binary_label",
|
| 17 |
+
"clinical_significance",
|
| 18 |
+
"site_type",
|
| 19 |
+
"gene",
|
| 20 |
+
"sample_id",
|
| 21 |
+
"aa_ref",
|
| 22 |
+
"aa_pos",
|
| 23 |
+
"aa_alt",
|
| 24 |
+
"mutation",
|
| 25 |
+
"protein_change",
|
| 26 |
+
"wt_window",
|
| 27 |
+
"mut_window",
|
| 28 |
+
"ptm_window",
|
| 29 |
+
"ref_match_fasta",
|
| 30 |
+
"nearest_ptm_pos",
|
| 31 |
+
"ptm_type",
|
| 32 |
+
"ptm_hit",
|
| 33 |
+
"ptm_distance",
|
| 34 |
+
"is_phosphorylation",
|
| 35 |
+
"is_acetylation",
|
| 36 |
+
"is_ubiquitination",
|
| 37 |
+
"domain_hit",
|
| 38 |
+
"domain_distance",
|
| 39 |
+
"gtex_gene_tpm_mean",
|
| 40 |
+
"gtex_gene_tpm_log1p",
|
| 41 |
+
"wt_embedding",
|
| 42 |
+
"mut_embedding",
|
| 43 |
+
"delta_embedding",
|
| 44 |
+
"ptm_embedding",
|
| 45 |
+
"ptm_delta_embedding",
|
| 46 |
+
"ptm_features",
|
| 47 |
+
"domain_features",
|
| 48 |
+
"gtex_features",
|
| 49 |
+
"state_perturbation_vector"
|
| 50 |
+
]
|
| 51 |
+
}
|