diff --git a/public/dlbc_tcga_pan_can_atlas_2018/case_lists/cases_methylation_all.txt b/public/dlbc_tcga_pan_can_atlas_2018/case_lists/cases_methylation_all.txt new file mode 100644 index 0000000000..74d772863b --- /dev/null +++ b/public/dlbc_tcga_pan_can_atlas_2018/case_lists/cases_methylation_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: dlbc_tcga_pan_can_atlas_2018 +stable_id: dlbc_tcga_pan_can_atlas_2018_methylation_all +case_list_name: Samples with methylation data +case_list_description: Samples with methylation data (48 samples) +case_list_category: all_cases_with_methylation_data +case_list_ids: TCGA-FA-8693-01 TCGA-FA-A4BB-01 TCGA-FA-A4XK-01 TCGA-FA-A6HN-01 TCGA-FA-A6HO-01 TCGA-FA-A7DS-01 TCGA-FA-A7Q1-01 TCGA-FA-A82F-01 TCGA-FA-A86F-01 TCGA-FF-8041-01 TCGA-FF-8042-01 TCGA-FF-8043-01 TCGA-FF-8046-01 TCGA-FF-8047-01 TCGA-FF-8061-01 TCGA-FF-8062-01 TCGA-FF-A7CQ-01 TCGA-FF-A7CR-01 TCGA-FF-A7CW-01 TCGA-FF-A7CX-01 TCGA-FM-8000-01 TCGA-G8-6324-01 TCGA-G8-6325-01 TCGA-G8-6326-01 TCGA-G8-6906-01 TCGA-G8-6907-01 TCGA-G8-6909-01 TCGA-G8-6914-01 TCGA-GR-7351-01 TCGA-GR-7353-01 TCGA-GR-A4D4-01 TCGA-GR-A4D5-01 TCGA-GR-A4D6-01 TCGA-GR-A4D9-01 TCGA-GS-A9TQ-01 TCGA-GS-A9TT-01 TCGA-GS-A9TU-01 TCGA-GS-A9TV-01 TCGA-GS-A9TW-01 TCGA-GS-A9TX-01 TCGA-GS-A9TY-01 TCGA-GS-A9TZ-01 TCGA-GS-A9U3-01 TCGA-GS-A9U4-01 TCGA-RQ-A68N-01 TCGA-RQ-A6JB-01 TCGA-RQ-AAAT-01 TCGA-VB-A8QN-01 \ No newline at end of file diff --git a/public/dlbc_tcga_pan_can_atlas_2018/case_lists/cases_methylation_hm450.txt b/public/dlbc_tcga_pan_can_atlas_2018/case_lists/cases_methylation_hm450.txt new file mode 100644 index 0000000000..114b6f0310 --- /dev/null +++ b/public/dlbc_tcga_pan_can_atlas_2018/case_lists/cases_methylation_hm450.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: dlbc_tcga_pan_can_atlas_2018 +stable_id: dlbc_tcga_pan_can_atlas_2018_methylation_hm450 +case_list_name: Samples with methylation data (HM450) +case_list_description: Samples with methylation (HM450) data (48 samples) +case_list_category: all_cases_with_methylation_data +case_list_ids: TCGA-FA-8693-01 TCGA-FA-A4BB-01 TCGA-FA-A4XK-01 TCGA-FA-A6HN-01 TCGA-FA-A6HO-01 TCGA-FA-A7DS-01 TCGA-FA-A7Q1-01 TCGA-FA-A82F-01 TCGA-FA-A86F-01 TCGA-FF-8041-01 TCGA-FF-8042-01 TCGA-FF-8043-01 TCGA-FF-8046-01 TCGA-FF-8047-01 TCGA-FF-8061-01 TCGA-FF-8062-01 TCGA-FF-A7CQ-01 TCGA-FF-A7CR-01 TCGA-FF-A7CW-01 TCGA-FF-A7CX-01 TCGA-FM-8000-01 TCGA-G8-6324-01 TCGA-G8-6325-01 TCGA-G8-6326-01 TCGA-G8-6906-01 TCGA-G8-6907-01 TCGA-G8-6909-01 TCGA-G8-6914-01 TCGA-GR-7351-01 TCGA-GR-7353-01 TCGA-GR-A4D4-01 TCGA-GR-A4D5-01 TCGA-GR-A4D6-01 TCGA-GR-A4D9-01 TCGA-GS-A9TQ-01 TCGA-GS-A9TT-01 TCGA-GS-A9TU-01 TCGA-GS-A9TV-01 TCGA-GS-A9TW-01 TCGA-GS-A9TX-01 TCGA-GS-A9TY-01 TCGA-GS-A9TZ-01 TCGA-GS-A9U3-01 TCGA-GS-A9U4-01 TCGA-RQ-A68N-01 TCGA-RQ-A6JB-01 TCGA-RQ-AAAT-01 TCGA-VB-A8QN-01 \ No newline at end of file diff --git a/public/dlbc_tcga_pan_can_atlas_2018/data_methylation_hm450.txt b/public/dlbc_tcga_pan_can_atlas_2018/data_methylation_hm450.txt new file mode 100644 index 0000000000..cb59196207 --- /dev/null +++ b/public/dlbc_tcga_pan_can_atlas_2018/data_methylation_hm450.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:418f4bd0e17629fa99ec49c7ec07a9dc0e8e810f6b85419d9c734a298d7fb616 +size 190097663 diff --git a/public/dlbc_tcga_pan_can_atlas_2018/meta_methylation_hm450.txt b/public/dlbc_tcga_pan_can_atlas_2018/meta_methylation_hm450.txt new file mode 100644 index 0000000000..8d1e987764 --- /dev/null +++ b/public/dlbc_tcga_pan_can_atlas_2018/meta_methylation_hm450.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: dlbc_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: METHYLATION +datatype: LIMIT-VALUE +stable_id: methylation_hm450 +profile_name: Methylation (HM450) +profile_description: Methylation beta-values (HM450 platform). For genes with multiple methylation probes, the probe least correlated with expression is selected. +data_filename: data_methylation_hm450.txt +show_profile_in_analysis_tab: true +value_sort_order: DESC +generic_entity_meta_properties: NAME,DESCRIPTION,TRANSCRIPT_ID \ No newline at end of file diff --git a/public/esca_tcga_pan_can_atlas_2018/case_lists/cases_methylation_all.txt b/public/esca_tcga_pan_can_atlas_2018/case_lists/cases_methylation_all.txt new file mode 100644 index 0000000000..6916e87ecb --- /dev/null +++ b/public/esca_tcga_pan_can_atlas_2018/case_lists/cases_methylation_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: esca_tcga_pan_can_atlas_2018 +stable_id: esca_tcga_pan_can_atlas_2018_methylation_all +case_list_name: Samples with methylation data +case_list_description: Samples with methylation data (182 samples) +case_list_category: all_cases_with_methylation_data +case_list_ids: TCGA-2H-A9GF-01 TCGA-2H-A9GH-01 TCGA-2H-A9GI-01 TCGA-2H-A9GJ-01 TCGA-2H-A9GK-01 TCGA-2H-A9GL-01 TCGA-2H-A9GM-01 TCGA-2H-A9GN-01 TCGA-2H-A9GO-01 TCGA-2H-A9GQ-01 TCGA-2H-A9GR-01 TCGA-IC-A6RE-01 TCGA-IG-A3I8-01 TCGA-IG-A3QL-01 TCGA-IG-A3Y9-01 TCGA-IG-A3YA-01 TCGA-IG-A3YB-01 TCGA-IG-A3YC-01 TCGA-IG-A4P3-01 TCGA-IG-A4QS-01 TCGA-IG-A4QT-01 TCGA-IG-A50L-01 TCGA-IG-A51D-01 TCGA-IG-A5B8-01 TCGA-IG-A5S3-01 TCGA-IG-A625-01 TCGA-IG-A6QS-01 TCGA-IG-A7DP-01 TCGA-IG-A8O2-01 TCGA-IG-A97H-01 TCGA-IG-A97I-01 TCGA-JY-A6F8-01 TCGA-JY-A6FA-01 TCGA-JY-A6FB-01 TCGA-JY-A6FD-01 TCGA-JY-A6FE-01 TCGA-JY-A6FG-01 TCGA-JY-A6FH-01 TCGA-JY-A938-01 TCGA-JY-A939-01 TCGA-JY-A93C-01 TCGA-JY-A93D-01 TCGA-JY-A93E-01 TCGA-JY-A93F-01 TCGA-KH-A6WC-01 TCGA-L5-A43C-01 TCGA-L5-A43E-01 TCGA-L5-A43H-01 TCGA-L5-A43I-01 TCGA-L5-A43J-01 TCGA-L5-A43M-01 TCGA-L5-A4OE-01 TCGA-L5-A4OF-01 TCGA-L5-A4OG-01 TCGA-L5-A4OH-01 TCGA-L5-A4OI-01 TCGA-L5-A4OJ-01 TCGA-L5-A4OM-01 TCGA-L5-A4ON-01 TCGA-L5-A4OO-01 TCGA-L5-A4OP-01 TCGA-L5-A4OQ-01 TCGA-L5-A4OR-01 TCGA-L5-A4OS-01 TCGA-L5-A4OT-01 TCGA-L5-A4OU-01 TCGA-L5-A4OW-01 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b/public/esca_tcga_pan_can_atlas_2018/case_lists/cases_methylation_hm450.txt new file mode 100644 index 0000000000..27d8d4b8f0 --- /dev/null +++ b/public/esca_tcga_pan_can_atlas_2018/case_lists/cases_methylation_hm450.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: esca_tcga_pan_can_atlas_2018 +stable_id: esca_tcga_pan_can_atlas_2018_methylation_hm450 +case_list_name: Samples with methylation data (HM450) +case_list_description: Samples with methylation (HM450) data (182 samples) +case_list_category: all_cases_with_methylation_data +case_list_ids: TCGA-2H-A9GF-01 TCGA-2H-A9GH-01 TCGA-2H-A9GI-01 TCGA-2H-A9GJ-01 TCGA-2H-A9GK-01 TCGA-2H-A9GL-01 TCGA-2H-A9GM-01 TCGA-2H-A9GN-01 TCGA-2H-A9GO-01 TCGA-2H-A9GQ-01 TCGA-2H-A9GR-01 TCGA-IC-A6RE-01 TCGA-IG-A3I8-01 TCGA-IG-A3QL-01 TCGA-IG-A3Y9-01 TCGA-IG-A3YA-01 TCGA-IG-A3YB-01 TCGA-IG-A3YC-01 TCGA-IG-A4P3-01 TCGA-IG-A4QS-01 TCGA-IG-A4QT-01 TCGA-IG-A50L-01 TCGA-IG-A51D-01 TCGA-IG-A5B8-01 TCGA-IG-A5S3-01 TCGA-IG-A625-01 TCGA-IG-A6QS-01 TCGA-IG-A7DP-01 TCGA-IG-A8O2-01 TCGA-IG-A97H-01 TCGA-IG-A97I-01 TCGA-JY-A6F8-01 TCGA-JY-A6FA-01 TCGA-JY-A6FB-01 TCGA-JY-A6FD-01 TCGA-JY-A6FE-01 TCGA-JY-A6FG-01 TCGA-JY-A6FH-01 TCGA-JY-A938-01 TCGA-JY-A939-01 TCGA-JY-A93C-01 TCGA-JY-A93D-01 TCGA-JY-A93E-01 TCGA-JY-A93F-01 TCGA-KH-A6WC-01 TCGA-L5-A43C-01 TCGA-L5-A43E-01 TCGA-L5-A43H-01 TCGA-L5-A43I-01 TCGA-L5-A43J-01 TCGA-L5-A43M-01 TCGA-L5-A4OE-01 TCGA-L5-A4OF-01 TCGA-L5-A4OG-01 TCGA-L5-A4OH-01 TCGA-L5-A4OI-01 TCGA-L5-A4OJ-01 TCGA-L5-A4OM-01 TCGA-L5-A4ON-01 TCGA-L5-A4OO-01 TCGA-L5-A4OP-01 TCGA-L5-A4OQ-01 TCGA-L5-A4OR-01 TCGA-L5-A4OS-01 TCGA-L5-A4OT-01 TCGA-L5-A4OU-01 TCGA-L5-A4OW-01 TCGA-L5-A4OX-01 TCGA-L5-A88S-01 TCGA-L5-A88V-01 TCGA-L5-A88W-01 TCGA-L5-A88Y-01 TCGA-L5-A88Z-01 TCGA-L5-A891-01 TCGA-L5-A893-01 TCGA-L5-A8NE-01 TCGA-L5-A8NF-01 TCGA-L5-A8NG-01 TCGA-L5-A8NH-01 TCGA-L5-A8NI-01 TCGA-L5-A8NJ-01 TCGA-L5-A8NK-01 TCGA-L5-A8NL-01 TCGA-L5-A8NM-01 TCGA-L5-A8NN-01 TCGA-L5-A8NQ-01 TCGA-L5-A8NR-01 TCGA-L5-A8NS-01 TCGA-L5-A8NT-01 TCGA-L5-A8NU-01 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TCGA-V5-A7RC-01 TCGA-V5-A7RE-01 TCGA-V5-AASV-01 TCGA-V5-AASW-01 TCGA-V5-AASX-01 TCGA-VR-A8EO-01 TCGA-VR-A8EP-01 TCGA-VR-A8EQ-01 TCGA-VR-A8ER-01 TCGA-VR-A8ET-01 TCGA-VR-A8EU-01 TCGA-VR-A8EW-01 TCGA-VR-A8EX-01 TCGA-VR-A8EY-01 TCGA-VR-A8EZ-01 TCGA-VR-A8Q7-01 TCGA-VR-AA4D-01 TCGA-VR-AA4G-01 TCGA-VR-AA7B-01 TCGA-VR-AA7D-01 TCGA-VR-AA7I-01 TCGA-X8-AAAR-01 TCGA-XP-A8T6-01 TCGA-XP-A8T7-01 TCGA-XP-A8T8-01 TCGA-Z6-A8JD-01 TCGA-Z6-A8JE-01 TCGA-Z6-A9VB-01 TCGA-Z6-AAPN-01 TCGA-ZR-A9CJ-01 \ No newline at end of file diff --git a/public/esca_tcga_pan_can_atlas_2018/data_methylation_hm450.txt b/public/esca_tcga_pan_can_atlas_2018/data_methylation_hm450.txt new file mode 100644 index 0000000000..8349f15d32 --- /dev/null +++ b/public/esca_tcga_pan_can_atlas_2018/data_methylation_hm450.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:2e2d53dfe47963f1d6324d755bcb79929aabb29ea0ef3ec3da729a7cce70d342 +size 678248760 diff --git a/public/esca_tcga_pan_can_atlas_2018/meta_methylation_hm450.txt b/public/esca_tcga_pan_can_atlas_2018/meta_methylation_hm450.txt new file mode 100644 index 0000000000..731581470e --- /dev/null +++ b/public/esca_tcga_pan_can_atlas_2018/meta_methylation_hm450.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: esca_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: METHYLATION +datatype: LIMIT-VALUE +stable_id: methylation_hm450 +profile_name: Methylation (HM450) +profile_description: Methylation beta-values (HM450 platform). For genes with multiple methylation probes, the probe least correlated with expression is selected. +data_filename: data_methylation_hm450.txt +show_profile_in_analysis_tab: true +value_sort_order: DESC +generic_entity_meta_properties: NAME,DESCRIPTION,TRANSCRIPT_ID \ No newline at end of file diff --git a/public/gbm_tcga_pan_can_atlas_2018/case_lists/cases_methylation_all.txt b/public/gbm_tcga_pan_can_atlas_2018/case_lists/cases_methylation_all.txt new file mode 100644 index 0000000000..33843ccd72 --- /dev/null +++ b/public/gbm_tcga_pan_can_atlas_2018/case_lists/cases_methylation_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: gbm_tcga_pan_can_atlas_2018 +stable_id: gbm_tcga_pan_can_atlas_2018_methylation_all +case_list_name: Samples with methylation data +case_list_description: Samples with methylation data (422 samples) +case_list_category: all_cases_with_methylation_data +case_list_ids: TCGA-02-2466-01 TCGA-02-2470-01 TCGA-02-2483-01 TCGA-02-2485-01 TCGA-02-2486-01 TCGA-06-1084-01 TCGA-06-1086-01 TCGA-06-1087-01 TCGA-06-1800-01 TCGA-06-1801-01 TCGA-06-1802-01 TCGA-06-1804-01 TCGA-06-1805-01 TCGA-06-1806-01 TCGA-06-2557-01 TCGA-06-2558-01 TCGA-06-2559-01 TCGA-06-2561-01 TCGA-06-2562-01 TCGA-06-2563-01 TCGA-06-2564-01 TCGA-06-2565-01 TCGA-06-2566-01 TCGA-06-2567-01 TCGA-06-2569-01 TCGA-06-2570-01 TCGA-06-5408-01 TCGA-06-5410-01 TCGA-06-5411-01 TCGA-06-5412-01 TCGA-06-5413-01 TCGA-06-5414-01 TCGA-06-5415-01 TCGA-06-5416-01 TCGA-06-5417-01 TCGA-06-5418-01 TCGA-06-5856-01 TCGA-06-5858-01 TCGA-06-5859-01 TCGA-06-6388-01 TCGA-06-6389-01 TCGA-06-6390-01 TCGA-06-6693-01 TCGA-06-6694-01 TCGA-06-6695-01 TCGA-06-6697-01 TCGA-06-6698-01 TCGA-06-6699-01 TCGA-06-6700-01 TCGA-06-6701-01 TCGA-06-A5U0-01 TCGA-06-A5U1-01 TCGA-06-A6S0-01 TCGA-06-A6S1-01 TCGA-06-A7TK-01 TCGA-06-A7TL-01 TCGA-12-1088-01 TCGA-12-1089-01 TCGA-12-1090-01 TCGA-12-1091-01 TCGA-12-1092-01 TCGA-12-1093-01 TCGA-12-1094-01 TCGA-12-1095-01 TCGA-12-1096-01 TCGA-12-1097-01 TCGA-12-1098-01 TCGA-12-1099-01 TCGA-12-1597-01 TCGA-12-1598-01 TCGA-12-1599-01 TCGA-12-1600-01 TCGA-12-1602-01 TCGA-12-3644-01 TCGA-12-3646-01 TCGA-12-3648-01 TCGA-12-3649-01 TCGA-12-3650-01 TCGA-12-3651-01 TCGA-12-3652-01 TCGA-12-3653-01 TCGA-12-5295-01 TCGA-12-5299-01 TCGA-12-5301-01 TCGA-14-1034-02 TCGA-14-1034-01 TCGA-14-1037-01 TCGA-14-1043-01 TCGA-14-1395-01 TCGA-14-1396-01 TCGA-14-1401-01 TCGA-14-1402-01 TCGA-14-1450-01 TCGA-14-1451-01 TCGA-14-1452-01 TCGA-14-1453-01 TCGA-14-1454-01 TCGA-14-1455-01 TCGA-14-1456-01 TCGA-14-1458-01 TCGA-14-1459-01 TCGA-14-1794-01 TCGA-14-1795-01 TCGA-14-1821-01 TCGA-14-1823-01 TCGA-14-1825-01 TCGA-14-1827-01 TCGA-14-1829-01 TCGA-14-2554-01 TCGA-14-2555-01 TCGA-14-3476-01 TCGA-14-3477-01 TCGA-14-4157-01 TCGA-15-1444-01 TCGA-15-1446-01 TCGA-15-1447-01 TCGA-15-1449-01 TCGA-16-1045-01 TCGA-16-1047-01 TCGA-16-1055-01 TCGA-16-1056-01 TCGA-16-1060-01 TCGA-16-1062-01 TCGA-16-1063-01 TCGA-16-1460-01 TCGA-19-1385-01 TCGA-19-1386-01 TCGA-19-1387-01 TCGA-19-1388-01 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TCGA-27-2527-01 TCGA-27-2528-01 TCGA-28-1746-01 TCGA-28-1747-01 TCGA-28-1749-01 TCGA-28-1750-01 TCGA-28-1751-01 TCGA-28-1752-01 TCGA-28-1753-01 TCGA-28-1755-01 TCGA-28-1756-01 TCGA-28-1757-01 TCGA-28-2499-01 TCGA-28-2502-01 TCGA-28-2506-01 TCGA-28-2509-01 TCGA-28-2513-01 TCGA-28-2514-01 TCGA-28-5204-01 TCGA-28-5207-01 TCGA-28-5208-01 TCGA-28-5209-01 TCGA-28-5211-01 TCGA-28-5213-01 TCGA-28-5214-01 TCGA-28-5215-01 TCGA-28-5216-01 TCGA-28-5218-01 TCGA-28-5219-01 TCGA-28-5220-01 TCGA-28-6450-01 TCGA-32-1970-01 TCGA-32-1973-01 TCGA-32-1976-01 TCGA-32-1977-01 TCGA-32-1978-01 TCGA-32-1979-01 TCGA-32-1980-01 TCGA-32-1982-01 TCGA-32-1986-01 TCGA-32-1987-01 TCGA-32-1991-01 TCGA-32-2491-01 TCGA-32-2494-01 TCGA-32-2495-01 TCGA-32-2615-01 TCGA-32-2616-01 TCGA-32-2632-01 TCGA-32-2634-01 TCGA-32-2638-01 TCGA-32-4208-01 TCGA-32-4209-01 TCGA-32-4210-01 TCGA-32-4211-01 TCGA-32-4213-01 TCGA-32-4719-01 TCGA-32-5222-01 TCGA-41-2571-01 TCGA-41-2572-01 TCGA-41-2573-01 TCGA-41-2575-01 TCGA-41-3392-01 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TCGA-06-0126-01 TCGA-02-0107-01 TCGA-02-0037-01 TCGA-06-0128-01 TCGA-06-0939-01 TCGA-12-0819-01 TCGA-16-0850-01 TCGA-02-0003-01 TCGA-19-0963-01 TCGA-19-0957-01 TCGA-14-0865-01 TCGA-06-0119-01 TCGA-14-0790-01 TCGA-06-0878-01 TCGA-02-0055-01 TCGA-02-0083-01 TCGA-06-0155-01 TCGA-06-0879-01 TCGA-02-0034-01 TCGA-28-2510-01 TCGA-02-0071-01 TCGA-02-0080-01 TCGA-06-0210-02 TCGA-02-0009-01 TCGA-02-0099-01 TCGA-02-0064-01 TCGA-14-0740-01 TCGA-12-0820-01 TCGA-02-0006-01 TCGA-06-0650-01 TCGA-02-0060-01 TCGA-16-0849-01 TCGA-19-0962-01 TCGA-06-0152-01 TCGA-12-0670-01 TCGA-02-0054-01 TCGA-12-0829-01 TCGA-28-2501-01 TCGA-06-0139-01 TCGA-16-1048-01 TCGA-06-0143-01 TCGA-02-0046-01 TCGA-19-0955-01 TCGA-14-0781-01 TCGA-02-0027-01 \ No newline at end of file diff --git a/public/gbm_tcga_pan_can_atlas_2018/case_lists/cases_methylation_hm450.txt b/public/gbm_tcga_pan_can_atlas_2018/case_lists/cases_methylation_hm450.txt new file mode 100644 index 0000000000..0e7a444344 --- /dev/null +++ b/public/gbm_tcga_pan_can_atlas_2018/case_lists/cases_methylation_hm450.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: gbm_tcga_pan_can_atlas_2018 +stable_id: gbm_tcga_pan_can_atlas_2018_methylation_hm450 +case_list_name: Samples with methylation data (HM450) +case_list_description: Samples with methylation (HM450) data (146 samples) +case_list_category: all_cases_with_methylation_data +case_list_ids: TCGA-06-0125-01 TCGA-06-0125-02 TCGA-06-0152-01 TCGA-06-0171-01 TCGA-06-0171-02 TCGA-06-0190-01 TCGA-06-0190-02 TCGA-06-0210-01 TCGA-06-0210-02 TCGA-06-0211-01 TCGA-06-0211-02 TCGA-06-0221-01 TCGA-06-0221-02 TCGA-06-0650-01 TCGA-06-1804-01 TCGA-06-1806-01 TCGA-06-5408-01 TCGA-06-5410-01 TCGA-06-5411-01 TCGA-06-5412-01 TCGA-06-5413-01 TCGA-06-5414-01 TCGA-06-5415-01 TCGA-06-5416-01 TCGA-06-5417-01 TCGA-06-5418-01 TCGA-06-5856-01 TCGA-06-5858-01 TCGA-06-5859-01 TCGA-06-6388-01 TCGA-06-6389-01 TCGA-06-6390-01 TCGA-06-6693-01 TCGA-06-6694-01 TCGA-06-6695-01 TCGA-06-6697-01 TCGA-06-6698-01 TCGA-06-6699-01 TCGA-06-6700-01 TCGA-06-6701-01 TCGA-06-A5U0-01 TCGA-06-A5U1-01 TCGA-06-A6S0-01 TCGA-06-A6S1-01 TCGA-06-A7TK-01 TCGA-06-A7TL-01 TCGA-12-5295-01 TCGA-12-5299-01 TCGA-12-5301-01 TCGA-14-0736-01 TCGA-14-0740-01 TCGA-14-0781-01 TCGA-14-0862-01 TCGA-14-1034-02 TCGA-14-1043-01 TCGA-14-1395-01 TCGA-14-1402-01 TCGA-14-1450-01 TCGA-15-1444-01 TCGA-19-0957-01 TCGA-19-1389-01 TCGA-19-4065-01 TCGA-19-5947-01 TCGA-19-5950-01 TCGA-19-5951-01 TCGA-19-5952-01 TCGA-19-5953-01 TCGA-19-5954-01 TCGA-19-5955-01 TCGA-19-5956-01 TCGA-19-5958-01 TCGA-19-5959-01 TCGA-19-5960-01 TCGA-19-A60I-01 TCGA-19-A6J4-01 TCGA-19-A6J5-01 TCGA-26-1442-01 TCGA-26-5132-01 TCGA-26-5133-01 TCGA-26-5134-01 TCGA-26-5135-01 TCGA-26-5136-01 TCGA-26-5139-01 TCGA-26-6173-01 TCGA-26-6174-01 TCGA-26-A7UX-01 TCGA-28-2501-01 TCGA-28-2510-01 TCGA-28-5204-01 TCGA-28-5207-01 TCGA-28-5208-01 TCGA-28-5209-01 TCGA-28-5211-01 TCGA-28-5213-01 TCGA-28-5214-01 TCGA-28-5215-01 TCGA-28-5216-01 TCGA-28-5218-01 TCGA-28-5219-01 TCGA-28-5220-01 TCGA-28-6450-01 TCGA-32-1979-01 TCGA-32-1980-01 TCGA-32-5222-01 TCGA-41-5651-01 TCGA-41-6646-01 TCGA-4W-AA9R-01 TCGA-4W-AA9S-01 TCGA-4W-AA9T-01 TCGA-74-6573-01 TCGA-74-6575-01 TCGA-74-6577-01 TCGA-74-6578-01 TCGA-74-6581-01 TCGA-74-6584-01 TCGA-76-4925-01 TCGA-76-4926-01 TCGA-76-4927-01 TCGA-76-4928-01 TCGA-76-4929-01 TCGA-76-4931-01 TCGA-76-4932-01 TCGA-76-4934-01 TCGA-76-4935-01 TCGA-76-6191-01 TCGA-76-6192-01 TCGA-76-6193-01 TCGA-76-6280-01 TCGA-76-6282-01 TCGA-76-6283-01 TCGA-76-6285-01 TCGA-76-6286-01 TCGA-76-6656-01 TCGA-76-6657-01 TCGA-76-6660-01 TCGA-76-6661-01 TCGA-76-6662-01 TCGA-76-6663-01 TCGA-76-6664-01 TCGA-81-5910-01 TCGA-81-5911-01 TCGA-87-5896-01 TCGA-OX-A56R-01 TCGA-RR-A6KA-01 TCGA-RR-A6KB-01 TCGA-RR-A6KC-01 \ No newline at end of file diff --git a/public/gbm_tcga_pan_can_atlas_2018/data_methylation_hm450.txt b/public/gbm_tcga_pan_can_atlas_2018/data_methylation_hm450.txt new file mode 100644 index 0000000000..7b70286807 --- /dev/null +++ b/public/gbm_tcga_pan_can_atlas_2018/data_methylation_hm450.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:594a130f12aad839a6c9b21284cd96b527ad8d860d6430ca4d29a5bd392acf5b +size 548518790 diff --git a/public/gbm_tcga_pan_can_atlas_2018/meta_methylation_hm450.txt b/public/gbm_tcga_pan_can_atlas_2018/meta_methylation_hm450.txt new file mode 100644 index 0000000000..5b2cf54c97 --- /dev/null +++ b/public/gbm_tcga_pan_can_atlas_2018/meta_methylation_hm450.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: gbm_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: METHYLATION +datatype: LIMIT-VALUE +stable_id: methylation_hm450 +profile_name: Methylation (HM450) +profile_description: Methylation beta-values (HM450 platform). For genes with multiple methylation probes, the probe least correlated with expression is selected. +data_filename: data_methylation_hm450.txt +show_profile_in_analysis_tab: true +value_sort_order: DESC +generic_entity_meta_properties: NAME,DESCRIPTION,TRANSCRIPT_ID \ No newline at end of file diff --git a/public/hnsc_tcga_pan_can_atlas_2018/case_lists/cases_methylation_all.txt b/public/hnsc_tcga_pan_can_atlas_2018/case_lists/cases_methylation_all.txt new file mode 100644 index 0000000000..ce9cb239fe --- /dev/null +++ b/public/hnsc_tcga_pan_can_atlas_2018/case_lists/cases_methylation_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018 +stable_id: hnsc_tcga_pan_can_atlas_2018_methylation_all +case_list_name: Samples with methylation data +case_list_description: Samples with methylation data (523 samples) +case_list_category: all_cases_with_methylation_data +case_list_ids: TCGA-4P-AA8J-01 TCGA-BA-4074-01 TCGA-BA-4076-01 TCGA-BA-4078-01 TCGA-BA-5149-01 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TCGA-TN-A7HL-01 TCGA-UF-A718-01 TCGA-UF-A719-01 TCGA-UF-A71A-01 TCGA-UF-A71B-01 TCGA-UF-A71D-01 TCGA-UF-A71E-01 TCGA-UF-A7J9-01 TCGA-UF-A7JA-01 TCGA-UF-A7JC-01 TCGA-UF-A7JD-01 TCGA-UF-A7JF-01 TCGA-UF-A7JH-01 TCGA-UF-A7JJ-01 TCGA-UF-A7JK-01 TCGA-UF-A7JO-01 TCGA-UF-A7JS-01 TCGA-UF-A7JT-01 TCGA-UF-A7JV-01 TCGA-UP-A6WW-01 TCGA-WA-A7GZ-01 TCGA-WA-A7H4-01 \ No newline at end of file diff --git a/public/hnsc_tcga_pan_can_atlas_2018/case_lists/cases_methylation_hm450.txt b/public/hnsc_tcga_pan_can_atlas_2018/case_lists/cases_methylation_hm450.txt new file mode 100644 index 0000000000..1a67425254 --- /dev/null +++ b/public/hnsc_tcga_pan_can_atlas_2018/case_lists/cases_methylation_hm450.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018 +stable_id: hnsc_tcga_pan_can_atlas_2018_methylation_hm450 +case_list_name: Samples with methylation data (HM450) +case_list_description: Samples with methylation (HM450) data (523 samples) +case_list_category: all_cases_with_methylation_data +case_list_ids: TCGA-4P-AA8J-01 TCGA-BA-4074-01 TCGA-BA-4076-01 TCGA-BA-4078-01 TCGA-BA-5149-01 TCGA-BA-5151-01 TCGA-BA-5152-01 TCGA-BA-5153-01 TCGA-BA-5555-01 TCGA-BA-5556-01 TCGA-BA-5557-01 TCGA-BA-5558-01 TCGA-BA-5559-01 TCGA-BA-6868-01 TCGA-BA-6869-01 TCGA-BA-6870-01 TCGA-BA-6871-01 TCGA-BA-6872-01 TCGA-BA-6873-01 TCGA-BA-7269-01 TCGA-BA-A4IF-01 TCGA-BA-A4IG-01 TCGA-BA-A4IH-01 TCGA-BA-A4II-01 TCGA-BA-A6D8-01 TCGA-BA-A6DA-01 TCGA-BA-A6DB-01 TCGA-BA-A6DD-01 TCGA-BA-A6DE-01 TCGA-BA-A6DF-01 TCGA-BA-A6DG-01 TCGA-BA-A6DI-01 TCGA-BA-A6DJ-01 TCGA-BA-A6DL-01 TCGA-BA-A8YP-01 TCGA-BB-4217-01 TCGA-BB-4223-01 TCGA-BB-4224-01 TCGA-BB-4225-01 TCGA-BB-4227-01 TCGA-BB-4228-01 TCGA-BB-7861-01 TCGA-BB-7862-01 TCGA-BB-7863-01 TCGA-BB-7864-01 TCGA-BB-7866-01 TCGA-BB-7870-01 TCGA-BB-7871-01 TCGA-BB-7872-01 TCGA-BB-8596-01 TCGA-BB-8601-01 TCGA-BB-A5HU-01 TCGA-BB-A5HY-01 TCGA-BB-A5HZ-01 TCGA-BB-A6UM-01 TCGA-BB-A6UO-01 TCGA-C9-A47Z-01 TCGA-C9-A480-01 TCGA-CN-4722-01 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a/public/hnsc_tcga_pan_can_atlas_2018/meta_methylation_hm450.txt b/public/hnsc_tcga_pan_can_atlas_2018/meta_methylation_hm450.txt new file mode 100644 index 0000000000..01f61532c0 --- /dev/null +++ b/public/hnsc_tcga_pan_can_atlas_2018/meta_methylation_hm450.txt @@ -0,0 +1,11 @@ +cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018 +genetic_alteration_type: GENERIC_ASSAY +generic_assay_type: METHYLATION +datatype: LIMIT-VALUE +stable_id: methylation_hm450 +profile_name: Methylation (HM450) +profile_description: Methylation beta-values (HM450 platform). For genes with multiple methylation probes, the probe least correlated with expression is selected. +data_filename: data_methylation_hm450.txt +show_profile_in_analysis_tab: true +value_sort_order: DESC +generic_entity_meta_properties: NAME,DESCRIPTION,TRANSCRIPT_ID \ No newline at end of file