diff --git a/public/brca_aurora_2022/case_lists/cases_cna.txt b/public/brca_aurora_2022/case_lists/cases_cna.txt new file mode 100644 index 0000000000..448c83f429 --- /dev/null +++ b/public/brca_aurora_2022/case_lists/cases_cna.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: brca_aurora_2022 +stable_id: brca_aurora_2022_cna +case_list_name: CNA +case_list_description: CNA samples +case_list_category: all_cases_with_cna_data +case_list_ids: AUR-AE5H-TTP1-A-1-1 AUR-AEPZ-TTM1-A-1-1 AUR-AER4-TTM2-A-1-1 AUR-AER6-TTM7-A-1-1 AUR-AERX-TTM1-A-1-1 AUR-AF99-TTP1-A-1-0 AUR-AFE4-TTM4-A-1-1 AUR-AFE5-TTM4-A-1-1 AUR-ADCB-TTM1-A-1-1 AUR-AEPZ-TTP1-A-1-1 AUR-AER4-TTP1-A-1-0 AUR-AER6-TTM10-A-1-1 AUR-AER6-TTM9-A-1-1 AUR-AER8-TTM1-A-1-1 AUR-AERX-TTP1-A-1-0 AUR-AF95-TTM1-A-1-1 AUR-AFE4-TTM5-A-1-1 AUR-AFE5-TTM5-A-1-1 AUR-ADCB-TTP1-A-13-0 AUR-AE6X-TTM1-A-1-1 AUR-AER6-TTM1-A-1-1 AUR-AER6-TTP1-A-1-0 AUR-AER8-TTM2-A-1-1 AUR-AF95-TTP1-A-1-0 AUR-AF9A-TTM1-A-1-1 AUR-AFE4-TTM6-A-1-1 AUR-AFE5-TTM6-A-1-1 AUR-AE6X-TTP1-A-1-0 AUR-AER2-TTM1-A-1-1 AUR-AER6-TTM2-A-1-1 AUR-AER8-TTP1-A-1-0 AUR-AERY-TTM1-A-1-1 AUR-AF9A-TTP1-A-1-0 AUR-AFE4-TTP1-A-1-0 AUR-AFE5-TTM7-A-1-1 AUR-AE5G-TTM1-A-1-1 AUR-AER2-TTM3-A-1-1 AUR-AER5-TTM4-A-1-1 AUR-AER6-TTM3-A-1-1 AUR-AER7-TTM1-A-1-1 AUR-AERY-TTP1-A-1-0 AUR-AF98-TTM1-A-1-1 AUR-AFE5-TTM8-A-1-1 AUR-AE5G-TTP1-A-1-1 AUR-AE6Y-TTM1-A-1-1 AUR-AER2-TTP1-A-1-1 AUR-AER5-TTM5-A-1-1 AUR-AER7-TTM2-A-1-1 AUR-AERW-TTM1-A-1-1 AUR-AF98-TTP1-A-1-0 AUR-AFE4-TTM1-A-1-1 AUR-AFE5-TTM10-A-1-1 AUR-AFE5-TTM9-A-1-1 AUR-AE6Y-TTP1-A-1-0 AUR-AER5-TTP2-A-1-1 AUR-AER6-TTM5-A-1-1 AUR-AER7-TTM4-A-1-1 AUR-AERW-TTP1-B-1-0 AUR-AF94-TTM1-A-1-1 AUR-AFE4-TTM2-A-1-1 AUR-AFE5-TTM1-A-1-1 AUR-AFE5-TTP1-A-1-0 AUR-AE5H-TTM1-A-1-1 AUR-AER4-TTM1-A-1-1 AUR-AER5-TTP3-A-1-0 AUR-AER6-TTM6-A-1-1 AUR-AER7-TTP1-A-1-0 AUR-AF94-TTP1-A-1-0 AUR-AF99-TTM1-A-1-1 AUR-AFE4-TTM3-A-1-1 AUR-AFE5-TTM2-A-1-1 AUR-AFE6-TTM1-A-1-1 AUR-AFEA-TTM2-A-1-1 AUR-AFEC-TTM3-A-1-1 AUR-AFKB-TTP1-A-10-0 AUR-AFR2-TTM1-A-1-1 AUR-AFSO-TTP1-A-8-0 AUR-AFUI-TTM1-A-1-0 AUR-AFE6-TTM2-A-1-1 AUR-AFE9-TTM1-A-1-1 AUR-AFEA-TTM3-A-1-1 AUR-AFEC-TTM4-A-1-1 AUR-AFR2-TTP1-A-1-1 AUR-AFR5-TTM1-A-1-1 AUR-AFUI-TTP1-A-1-0 AUR-AG0M-TTM1-A-2-1 AUR-AFE6-TTP1-A-1-0 AUR-AFE9-TTM2-A-1-1 AUR-AFEA-TTM4-A-1-1 AUR-AFEC-TTM5-A-1-1 AUR-AFKD-TTM1-A-1-1 AUR-AFR5-TTP1-A-1-1 AUR-AFSP-TTM1-A-8-0 AUR-AFUM-TTM1-A-1-1 AUR-AG0M-TTP1-A-2-0 AUR-AFE9-TTM3-A-1-1 AUR-AFEA-TTM6-A-1-0 AUR-AFEC-TTM6-A-1-1 AUR-AFKD-TTP1-A-1-1 AUR-AFR3-TTM1-A-1-1 AUR-AFSP-TTP1-A-8-0 AUR-AFUK-TTM1-A-1-0 AUR-AFUM-TTP1-A-1-0 AUR-AFUP-TTM1-A-1-1 AUR-AFE7-TTM1-A-1-1 AUR-AFE9-TTM4-A-1-1 AUR-AFEA-TTP1-A-1-0 AUR-AFEC-TTP1-A-1-0 AUR-AFR3-TTP1-A-2-1 AUR-AFSL-TTM1-A-8-0 AUR-AFUK-TTM2-A-1-0 AUR-AFUP-TTP1-A-1-0 AUR-AG0N-TTM1-A-1-1 AUR-AFE7-TTM2-A-1-1 AUR-AFE9-TTP1-A-1-0 AUR-AFKF-TTM1-A-1-1 AUR-AFSL-TTP1-A-8-0 AUR-AFUG-TTM1-A-1-1 AUR-AFUK-TTP1-A-1-0 AUR-AFUN-TTM1-A-1-0 AUR-AG0N-TTP1-A-1-0 AUR-AFE7-TTM3-A-1-1 AUR-AFKF-TTP1-A-10-0 AUR-AFR4-TTM1-A-1-1 AUR-AFUN-TTP1-A-1-0 AUR-AG0J-TTM1-A-1-0 AUR-AFE7-TTP2-A-1-1 AUR-AFEA-TTM1-A-1-1 AUR-AFEC-TTM1-A-1-1 AUR-AFKB-TTM1-A-1-1 AUR-AFR4-TTP1-A-1-1 AUR-AFSO-TTM1-A-8-0 AUR-AG0J-TTP1-A-1-0 AUR-AG12-TTM1-A-1-1 AUR-AG12-TTP1-A-1-0 diff --git a/public/brca_aurora_2022/case_lists/cases_methylation.txt b/public/brca_aurora_2022/case_lists/cases_methylation.txt new file mode 100644 index 0000000000..7f42b07197 --- /dev/null +++ b/public/brca_aurora_2022/case_lists/cases_methylation.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: brca_aurora_2022 +stable_id: brca_aurora_2022_methylation +case_list_name: METHYLATION +case_list_description: METHYLATION samples +case_list_category: all_cases_with_methylation_data +case_list_ids: AUR-AD9E-TTM1-A-2-1 AUR-AD9E-TTM2-A-1-1 AUR-AD9F-TTM1-A-1-1 AUR-AD9F-TTM2-A-2-1 AUR-AD9F-TTM3-A-1-1 AUR-AD9G-TTM1-A-2-1 AUR-AD9G-TTM2-A-1-1 AUR-AD9G-TTM3-A-1-1 AUR-AD9G-TTP1-B-4-0 AUR-AD9H-TTM1-A-2-1 AUR-AD9H-TTM2-A-1-1 AUR-AD9H-TTM3-A-1-1 AUR-AD9I-TTM3-A-1-1 AUR-ADCB-TTM1-A-1-1 AUR-ADCB-TTP1-A-13-0 AUR-AE5G-TTM1-A-1-1 AUR-AE5G-TTP1-A-1-1 AUR-AE5H-TTM1-A-1-1 AUR-AE5H-TTP1-A-1-1 AUR-AE6X-TTM1-A-1-1 AUR-AE6Y-TTM1-A-1-1 AUR-AE6Y-TTP1-A-1-0 AUR-AEPZ-TTM1-A-1-1 AUR-AEPZ-TTP1-A-1-1 AUR-AER2-TTM1-A-1-1 AUR-AER2-TTM3-A-1-1 AUR-AER2-TTP1-A-1-1 AUR-AER4-TTM1-A-1-1 AUR-AER4-TTM2-A-1-1 AUR-AER5-TTM4-A-1-1 AUR-AER5-TTM5-A-1-1 AUR-AER5-TTP2-A-1-1 AUR-AER5-TTP3-A-1-0 AUR-AER6-TTM1-A-1-1 AUR-AER6-TTM10-A-1-1 AUR-AER6-TTM2-A-1-1 AUR-AER6-TTM3-A-1-1 AUR-AER6-TTM5-A-1-1 AUR-AER6-TTM6-A-1-1 AUR-AER6-TTM7-A-1-1 AUR-AER6-TTM9-A-1-1 AUR-AER6-TTP1-A-1-0 AUR-AER7-TTM1-A-1-1 AUR-AER7-TTM2-A-1-1 AUR-AER7-TTM4-A-1-1 AUR-AER8-TTM1-A-1-1 AUR-AER8-TTM2-A-1-1 AUR-AER8-TTP1-A-1-0 AUR-AERW-TTP1-B-1-0 AUR-AERX-TTP1-A-1-0 AUR-AERY-TTM1-A-1-1 AUR-AF94-TTM1-A-1-1 AUR-AF94-TTP1-A-1-0 AUR-AF95-TTM1-A-1-1 AUR-AF95-TTP1-A-1-0 AUR-AF98-TTM1-A-1-1 AUR-AF98-TTP1-A-1-0 AUR-AF99-TTM1-A-1-1 AUR-AF9A-TTM1-A-1-1 AUR-AF9A-TTP1-A-1-0 AUR-AFE4-TTM1-A-1-1 AUR-AFE4-TTM2-A-1-1 AUR-AFE4-TTM3-A-1-1 AUR-AFE4-TTM4-A-1-1 AUR-AFE4-TTM5-A-1-1 AUR-AFE4-TTM6-A-1-1 AUR-AFE5-TTM1-A-1-1 AUR-AFE5-TTM10-A-1-1 AUR-AFE5-TTM2-A-1-1 AUR-AFE5-TTM4-A-1-1 AUR-AFE5-TTM5-A-1-1 AUR-AFE5-TTM6-A-1-1 AUR-AFE5-TTM7-A-1-1 AUR-AFE5-TTM8-A-1-1 AUR-AFE5-TTM9-A-1-1 AUR-AFE5-TTP1-A-1-0 AUR-AFE6-TTM1-A-1-1 AUR-AFE6-TTM2-A-1-1 AUR-AFE7-TTM1-A-1-1 AUR-AFE7-TTM2-A-1-1 AUR-AFE7-TTM3-A-1-1 AUR-AFE7-TTP2-A-1-1 AUR-AFE9-TTM1-A-1-1 AUR-AFE9-TTM3-A-1-1 AUR-AFE9-TTM4-A-1-1 AUR-AFEA-TTM1-A-1-1 AUR-AFEA-TTM2-A-1-1 AUR-AFEA-TTM3-A-1-1 AUR-AFEA-TTM4-A-1-1 AUR-AFEA-TTM6-A-1-0 AUR-AFEA-TTP2-A-1-0 AUR-AFEC-TTM1-A-1-1 AUR-AFEC-TTM3-A-1-1 AUR-AFEC-TTM4-A-1-1 AUR-AFEC-TTM6-A-1-1 AUR-AFEC-TTP1-A-1-0 AUR-AFKB-TTM1-A-1-1 AUR-AFKB-TTP1-A-10-0 AUR-AFKD-TTM1-A-1-1 AUR-AFKD-TTP1-A-1-1 AUR-AFKF-TTM1-A-1-1 AUR-AFKF-TTP1-A-10-0 AUR-AFR2-TTM1-A-1-1 AUR-AFR2-TTP1-A-1-1 AUR-AFR3-TTM1-A-1-1 AUR-AFR3-TTP1-A-2-1 AUR-AFR4-TTM1-A-1-1 AUR-AFR5-TTM1-A-1-1 AUR-AFR5-TTP1-A-1-1 AUR-AFSL-TTM1-A-8-0 AUR-AFSL-TTP1-A-8-0 AUR-AFSO-TTM1-A-8-0 AUR-AFSO-TTP1-A-8-0 AUR-AFUG-TTM1-A-1-1 AUR-AFUI-TTM1-A-1-0 AUR-AFUI-TTP1-A-1-0 AUR-AFUK-TTM1-A-1-0 AUR-AFUK-TTM2-A-1-0 AUR-AFUK-TTP1-A-1-0 AUR-AFUL-TTM1-A-1-1 AUR-AFUL-TTP1-A-1-1 AUR-AFUM-TTM1-A-1-1 AUR-AFUN-TTM1-A-1-0 AUR-AFUN-TTP1-A-1-0 AUR-AFUP-TTM1-A-1-1 AUR-AFUP-TTP1-A-1-0 AUR-AG0J-TTM1-A-1-0 AUR-AG0J-TTP1-A-1-0 AUR-AG0M-TTM1-A-2-1 AUR-AG0N-TTM1-A-1-1 AUR-AG0N-TTP1-A-1-0 diff --git a/public/brca_aurora_2022/case_lists/cases_rna_seq_mrna.txt b/public/brca_aurora_2022/case_lists/cases_rna_seq_mrna.txt new file mode 100644 index 0000000000..dc184c0eb3 --- /dev/null +++ b/public/brca_aurora_2022/case_lists/cases_rna_seq_mrna.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: brca_aurora_2022 +stable_id: brca_aurora_2022_rna_seq_mrna +case_list_name: Samples with mRNA (log2 transformed z-Scores) data +case_list_description: Samples with CNV (log2 transformed z-Scores) data +case_list_category: all_cases_with_mrna_rnaseq_data +case_list_ids: AUR-AFEA-TTP1-A-1-0 AUR-AFEA-TTM4-A-1-1 AUR-AFEA-TTM2-A-1-1 AUR-AFEA-TTM1-A-1-1 AUR-AFEA-TTM3-A-1-1 AUR-AFEA-TTM6-A-1-0 AUR-AFE7-TTP2-A-1-1 AUR-AFE7-TTM2-A-1-1 AUR-AFE7-TTM1-A-1-1 AUR-AFE7-TTM3-A-1-1 AUR-AD9G-TTP1-B-4-0 AUR-AD9G-TTM2-A-1-1 AUR-AD9G-TTM3-A-1-1 AUR-AFE5-TTP1-A-1-0 AUR-AFE5-TTM4-A-1-1 AUR-AFE5-TTM9-A-1-1 AUR-AG0N-TTP1-A-1-0 AUR-AG0N-TTM1-A-1-1 AUR-AG0M-TTP1-A-2-0 AUR-AG0M-TTM1-A-2-1 AUR-AG0J-TTP1-A-1-0 AUR-AG0J-TTM1-A-1-0 AUR-AFSP-TTP1-A-8-0 AUR-AFSP-TTM1-A-8-0 AUR-AF9A-TTP1-A-1-0 AUR-AF9A-TTM1-A-1-1 AUR-AF98-TTP1-A-1-0 AUR-AF98-TTM1-A-1-1 AUR-AF95-TTP1-A-1-0 AUR-AF95-TTM1-A-1-1 AUR-AFSL-TTP1-A-8-0 AUR-AFSL-TTM1-A-8-0 AUR-AFR5-TTP1-A-1-1 AUR-AFR5-TTM1-A-1-1 AUR-AE6Y-TTP1-A-1-0 AUR-AE6Y-TTM1-A-1-1 AUR-AE5H-TTP1-A-1-1 AUR-AE5H-TTM1-A-1-1 AUR-AFUI-TTP1-A-1-0 AUR-AFUI-TTM1-A-1-0 AUR-AER7-TTP1-A-1-0 AUR-AER7-TTM4-A-1-1 AUR-AER6-TTP1-A-1-0 AUR-AER6-TTM2-A-1-1 AUR-AER6-TTM3-A-1-1 AUR-AER6-TTM7-A-1-1 AUR-AER6-TTM9-A-1-1 AUR-AER6-TTM6-A-1-1 AUR-AER6-TTM5-A-1-1 AUR-AER6-TTM1-A-1-1 AUR-AER6-TTM10-A-1-1 AUR-AFEC-TTP2-A-1-1 AUR-AFEC-TTM3-A-1-1 AUR-AFEC-TTM4-A-1-1 AUR-AFEC-TTM6-A-1-1 AUR-AG12-TTP1-A-1-0 AUR-AG12-TTM1-A-1-1 AUR-AERX-TTP1-A-1-0 AUR-AERX-TTM1-A-1-1 AUR-AERW-TTP1-B-1-0 AUR-AERW-TTM1-A-1-1 AUR-AFSO-TTP1-A-8-0 AUR-AFSO-TTM1-A-8-0 AUR-AFR3-TTP1-A-2-1 AUR-AFR3-TTM1-A-1-1 AUR-AE5G-TTP1-A-1-1 AUR-AE5G-TTM1-A-1-1 AUR-AF94-TTP1-A-1-0 AUR-AF94-TTM1-A-1-1 AUR-AFE4-TTP1-A-1-0 AUR-AFE4-TTM1-A-1-1 AUR-AFE4-TTM6-A-1-1 AUR-AFE4-TTM5-A-1-1 AUR-AFUN-TTP1-A-1-0 AUR-AFUN-TTM1-A-1-0 AUR-AFUL-TTP1-A-1-1 AUR-AFUL-TTM1-A-1-1 AUR-AFKB-TTP1-A-10-0 AUR-AFKB-TTM1-A-1-1 AUR-AEPZ-TTP1-A-1-1 AUR-AEPZ-TTM1-A-1-1 AUR-AER8-TTP1-A-1-0 AUR-AER8-TTM2-A-1-1 AUR-AFKF-TTP1-A-10-0 AUR-AFKF-TTM1-A-1-1 AUR-AFUM-TTP1-A-1-0 AUR-AFUM-TTM1-A-1-1 AUR-AFE9-TTP1-A-1-0 AUR-AFE9-TTM1-A-1-1 AUR-AFE9-TTM4-A-1-1 AUR-AFE9-TTM2-A-1-1 AUR-AFE9-TTM3-A-1-1 AUR-AER2-TTP1-A-1-1 AUR-AER2-TTM3-A-1-1 AUR-AER2-TTM1-A-1-1 AUR-AFE6-TTP1-A-1-0 AUR-AFE6-TTM2-A-1-1 AUR-AFE6-TTM1-A-1-1 AUR-AFR4-TTP1-A-1-1 AUR-AFR4-TTM1-A-1-1 AUR-AE6X-TTP1-A-1-0 AUR-AE6X-TTM1-A-1-1 AUR-AFKD-TTP1-A-1-1 AUR-AER4-TTP1-A-1-0 AUR-AD9J-TTP1-B-4-0 AUR-AFUO-TTP1-A-1-0 AUR-AFR2-TTP1-A-1-1 AUR-AERY-TTM1-A-1-1 AUR-ADCB-TTM1-A-1-1 AUR-AD9I-TTM3-A-1-1 AUR-AD9E-TTM1-A-1-1 AUR-AFUP-TTM1-A-1-1 AUR-AFUK-TTM2-A-1-0 AUR-AD9H-TTM1-A-2-1 AUR-AD9E-TTM4-A-1-1 AUR-AD9E-TTM2-A-1-1 AUR-AFUK-TTM1-A-1-0 AUR-AD9H-TTM3-A-1-1 AUR-AD9H-TTM2-A-1-1 AUR-AD9F-TTM3-A-1-1 AUR-AD9F-TTM1-A-1-1 AUR-AD9F-TTM2-A-1-1 AUR-AFUG-TTM1-A-1-1 diff --git a/public/brca_aurora_2022/case_lists/cases_samples_all.txt b/public/brca_aurora_2022/case_lists/cases_samples_all.txt new file mode 100644 index 0000000000..8e3d031e16 --- /dev/null +++ b/public/brca_aurora_2022/case_lists/cases_samples_all.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: brca_aurora_2022 +stable_id: brca_aurora_2022_all +case_list_name: All samples +case_list_description: All samples +case_list_category: all_cases_in_study +case_list_ids: AUR-AD9E-TTM1-A-1-1 AUR-AD9E-TTM1-A-2-1 AUR-AD9E-TTM2-A-1-1 AUR-AD9E-TTM4-A-1-1 AUR-AD9F-TTM1-A-1-1 AUR-AD9F-TTM2-A-1-1 AUR-AD9F-TTM2-A-2-1 AUR-AD9F-TTM3-A-1-1 AUR-AD9G-TTM1-A-1-1 AUR-AD9G-TTM1-A-2-1 AUR-AD9G-TTM2-A-1-1 AUR-AD9G-TTM3-A-1-1 AUR-AD9G-TTP1-B-4-0 AUR-AD9H-TTM1-A-2-1 AUR-AD9H-TTM2-A-1-1 AUR-AD9H-TTM3-A-1-1 AUR-AD9I-TTM3-A-1-1 AUR-AD9J-TTP1-B-4-0 AUR-ADCB-TTM1-A-1-1 AUR-ADCB-TTP1-A-13-0 AUR-AE5G-TTM1-A-1-1 AUR-AE5G-TTP1-A-1-1 AUR-AE5H-TTM1-A-1-1 AUR-AE5H-TTP1-A-1-1 AUR-AE6X-TTM1-A-1-1 AUR-AE6X-TTP1-A-1-0 AUR-AE6Y-TTM1-A-1-1 AUR-AE6Y-TTP1-A-1-0 AUR-AEPZ-TTM1-A-1-1 AUR-AEPZ-TTP1-A-1-1 AUR-AER2-TTM1-A-1-1 AUR-AER2-TTM3-A-1-1 AUR-AER2-TTP1-A-1-1 AUR-AER4-TTM1-A-1-1 AUR-AER4-TTM2-A-1-1 AUR-AER4-TTP1-A-1-0 AUR-AER5-TTM4-A-1-1 AUR-AER5-TTM5-A-1-1 AUR-AER5-TTP2-A-1-1 AUR-AER5-TTP3-A-1-0 AUR-AER6-TTM1-A-1-1 AUR-AER6-TTM10-A-1-1 AUR-AER6-TTM2-A-1-1 AUR-AER6-TTM3-A-1-1 AUR-AER6-TTM5-A-1-1 AUR-AER6-TTM6-A-1-1 AUR-AER6-TTM7-A-1-1 AUR-AER6-TTM9-A-1-1 AUR-AER6-TTP1-A-1-0 AUR-AER7-TTM1-A-1-1 AUR-AER7-TTM2-A-1-1 AUR-AER7-TTM4-A-1-1 AUR-AER7-TTP1-A-1-0 AUR-AER8-TTM1-A-1-1 AUR-AER8-TTM2-A-1-1 AUR-AER8-TTP1-A-1-0 AUR-AERW-TTM1-A-1-1 AUR-AERW-TTP1-B-1-0 AUR-AERX-TTM1-A-1-1 AUR-AERX-TTP1-A-1-0 AUR-AERY-TTM1-A-1-1 AUR-AERY-TTP1-A-1-0 AUR-AF94-TTM1-A-1-1 AUR-AF94-TTP1-A-1-0 AUR-AF95-TTM1-A-1-1 AUR-AF95-TTP1-A-1-0 AUR-AF98-TTM1-A-1-1 AUR-AF98-TTP1-A-1-0 AUR-AF99-TTM1-A-1-1 AUR-AF99-TTP1-A-1-0 AUR-AF9A-TTM1-A-1-1 AUR-AF9A-TTP1-A-1-0 AUR-AFE4-TTM1-A-1-1 AUR-AFE4-TTM2-A-1-1 AUR-AFE4-TTM3-A-1-1 AUR-AFE4-TTM4-A-1-1 AUR-AFE4-TTM5-A-1-1 AUR-AFE4-TTM6-A-1-1 AUR-AFE4-TTP1-A-1-0 AUR-AFE5-TTM1-A-1-1 AUR-AFE5-TTM10-A-1-1 AUR-AFE5-TTM2-A-1-1 AUR-AFE5-TTM4-A-1-1 AUR-AFE5-TTM5-A-1-1 AUR-AFE5-TTM6-A-1-1 AUR-AFE5-TTM7-A-1-1 AUR-AFE5-TTM8-A-1-1 AUR-AFE5-TTM9-A-1-1 AUR-AFE5-TTP1-A-1-0 AUR-AFE6-TTM1-A-1-1 AUR-AFE6-TTM2-A-1-1 AUR-AFE6-TTP1-A-1-0 AUR-AFE7-TTM1-A-1-1 AUR-AFE7-TTM2-A-1-1 AUR-AFE7-TTM3-A-1-1 AUR-AFE7-TTP2-A-1-1 AUR-AFE9-TTM1-A-1-1 AUR-AFE9-TTM2-A-1-1 AUR-AFE9-TTM3-A-1-1 AUR-AFE9-TTM4-A-1-1 AUR-AFE9-TTP1-A-1-0 AUR-AFEA-TTM1-A-1-1 AUR-AFEA-TTM2-A-1-1 AUR-AFEA-TTM3-A-1-1 AUR-AFEA-TTM4-A-1-1 AUR-AFEA-TTM6-A-1-0 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AUR-AG0N-TTP1-A-1-0 AUR-AG12-TTM1-A-1-1 AUR-AG12-TTP1-A-1-0 diff --git a/public/brca_aurora_2022/case_lists/mutation_sequenced.txt b/public/brca_aurora_2022/case_lists/mutation_sequenced.txt new file mode 100644 index 0000000000..819327289c --- /dev/null +++ b/public/brca_aurora_2022/case_lists/mutation_sequenced.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: brca_aurora_2022 +stable_id: brca_aurora_2022_sequenced +case_list_name: Mutations +case_list_description: Sample Mutations +case_list_category: all_cases_with_mutation_data +case_list_ids: AUR-AD9E-TTM1-A-1-1 AUR-AD9E-TTM2-A-1-1 AUR-AD9E-TTM4-A-1-1 AUR-AD9G-TTM1-A-1-1 AUR-AD9G-TTM2-A-1-1 AUR-AD9G-TTM3-A-1-1 AUR-AD9G-TTP1-B-4-0 AUR-AD9I-TTM3-A-1-1 AUR-ADCB-TTM1-A-1-1 AUR-ADCB-TTP1-A-13-0 AUR-AE5G-TTM1-A-1-1 AUR-AE5G-TTP1-A-1-1 AUR-AE5H-TTM1-A-1-1 AUR-AE5H-TTP1-A-1-1 AUR-AE6X-TTM1-A-1-1 AUR-AE6X-TTP1-A-1-0 AUR-AE6Y-TTM1-A-1-1 AUR-AE6Y-TTP1-A-1-0 AUR-AEPZ-TTM1-A-1-1 AUR-AEPZ-TTP1-A-1-1 AUR-AER2-TTM1-A-1-1 AUR-AER2-TTM3-A-1-1 AUR-AER2-TTP1-A-1-1 AUR-AER4-TTM1-A-1-1 AUR-AER4-TTM2-A-1-1 AUR-AER4-TTP1-A-1-0 AUR-AER5-TTM4-A-1-1 AUR-AER5-TTM5-A-1-1 AUR-AER5-TTP2-A-1-1 AUR-AER5-TTP3-A-1-0 AUR-AER6-TTM1-A-1-1 AUR-AER6-TTM10-A-1-1 AUR-AER6-TTM2-A-1-1 AUR-AER6-TTM3-A-1-1 AUR-AER6-TTM5-A-1-1 AUR-AER6-TTM6-A-1-1 AUR-AER6-TTM7-A-1-1 AUR-AER6-TTM9-A-1-1 AUR-AER6-TTP1-A-1-0 AUR-AER7-TTM1-A-1-1 AUR-AER7-TTM2-A-1-1 AUR-AER7-TTM4-A-1-1 AUR-AER8-TTM1-A-1-1 AUR-AER8-TTM2-A-1-1 AUR-AER8-TTP1-A-1-0 AUR-AERW-TTM1-A-1-1 AUR-AERW-TTP1-B-1-0 AUR-AERX-TTP1-A-1-0 AUR-AERY-TTM1-A-1-1 AUR-AERY-TTP1-A-1-0 AUR-AF94-TTM1-A-1-1 AUR-AF94-TTP1-A-1-0 AUR-AF95-TTM1-A-1-1 AUR-AF95-TTP1-A-1-0 AUR-AF98-TTM1-A-1-1 AUR-AF98-TTP1-A-1-0 AUR-AF99-TTM1-A-1-1 AUR-AF99-TTP1-A-1-0 AUR-AF9A-TTM1-A-1-1 AUR-AF9A-TTP1-A-1-0 AUR-AFE4-TTM1-A-1-1 AUR-AFE4-TTM2-A-1-1 AUR-AFE4-TTM3-A-1-1 AUR-AFE4-TTM4-A-1-1 AUR-AFE4-TTM5-A-1-1 AUR-AFE4-TTM6-A-1-1 AUR-AFE4-TTP1-A-1-0 AUR-AFE5-TTM1-A-1-1 AUR-AFE5-TTM10-A-1-1 AUR-AFE5-TTM2-A-1-1 AUR-AFE5-TTM4-A-1-1 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AUR-AFUK-TTM1-A-1-0 AUR-AFUK-TTM2-A-1-0 AUR-AFUM-TTM1-A-1-1 AUR-AFUM-TTP1-A-1-0 AUR-AFUN-TTM1-A-1-0 AUR-AFUN-TTP1-A-1-0 AUR-AFUP-TTM1-A-1-1 AUR-AFUP-TTP1-A-1-0 AUR-AG0J-TTM1-A-1-0 AUR-AG0J-TTP1-A-1-0 AUR-AG0M-TTM1-A-2-1 AUR-AG0N-TTM1-A-1-1 AUR-AG12-TTM1-A-1-1 AUR-AG12-TTP1-A-1-0 diff --git a/public/brca_aurora_2022/data_chemo.txt b/public/brca_aurora_2022/data_chemo.txt new file mode 100644 index 0000000000..1244ec3fd8 --- /dev/null +++ b/public/brca_aurora_2022/data_chemo.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:93becff5bf13102b7f993409219401f3db807e22f9197eca26ad28a66025d270 +size 2111 diff --git a/public/brca_aurora_2022/data_clinical_patient.txt b/public/brca_aurora_2022/data_clinical_patient.txt new file mode 100644 index 0000000000..94668f07e9 --- /dev/null +++ b/public/brca_aurora_2022/data_clinical_patient.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:09253fa0c1574437547fe27285583f6bbb164636723494cf856fa72fba85250c +size 289 diff --git a/public/brca_aurora_2022/data_clinical_sample.txt b/public/brca_aurora_2022/data_clinical_sample.txt new file mode 100644 index 0000000000..bd94895261 --- /dev/null +++ b/public/brca_aurora_2022/data_clinical_sample.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:eb93b508f16291ce9df6cea9fcb40a79feaa51555c2acc93b3e3c5e6d0da9b17 +size 23985 diff --git a/public/brca_aurora_2022/data_cna_hg38.seg b/public/brca_aurora_2022/data_cna_hg38.seg new file mode 100644 index 0000000000..6ac29e79aa --- /dev/null +++ b/public/brca_aurora_2022/data_cna_hg38.seg @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:3b16fd101597962be07caa84915e88aaef71cc9e59ac13335bfef51ff8db9607 +size 5583866 diff --git a/public/brca_aurora_2022/data_log2_cna.txt b/public/brca_aurora_2022/data_log2_cna.txt new file mode 100644 index 0000000000..893c3407a4 --- /dev/null +++ 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a/public/brca_aurora_2022/data_mrna_seq_rsem_zscores_ref_all_samples.txt b/public/brca_aurora_2022/data_mrna_seq_rsem_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..2fde87ccbb --- /dev/null +++ b/public/brca_aurora_2022/data_mrna_seq_rsem_zscores_ref_all_samples.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:19dbe64629f6d5148e474d562a83dad29d2a839afcff723401af975e6edcff48 +size 14960475 diff --git a/public/brca_aurora_2022/data_mutations.txt b/public/brca_aurora_2022/data_mutations.txt new file mode 100644 index 0000000000..a118c3c4eb --- /dev/null +++ b/public/brca_aurora_2022/data_mutations.txt @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:113eab7399ae8f5eb9759a836a4186d76eda48b76a07aca457538b29b92f2f02 +size 30162398 diff --git a/public/brca_aurora_2022/data_resource_definition.txt b/public/brca_aurora_2022/data_resource_definition.txt new file mode 100644 index 0000000000..27f7c9b579 --- /dev/null +++ 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b/public/brca_aurora_2022/meta_chemo.txt new file mode 100644 index 0000000000..7adeec902b --- /dev/null +++ b/public/brca_aurora_2022/meta_chemo.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: brca_aurora_us +genetic_alteration_type: CLINICAL +datatype: TIMELINE +data_filename: data_chemo.txt diff --git a/public/brca_aurora_2022/meta_clinical_patient.txt b/public/brca_aurora_2022/meta_clinical_patient.txt new file mode 100644 index 0000000000..b8de00d6b3 --- /dev/null +++ b/public/brca_aurora_2022/meta_clinical_patient.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: brca_aurora_2022 +genetic_alteration_type: CLINICAL +datatype: PATIENT_ATTRIBUTES +data_filename: data_clinical_patient.txt diff --git a/public/brca_aurora_2022/meta_clinical_sample.txt b/public/brca_aurora_2022/meta_clinical_sample.txt new file mode 100644 index 0000000000..b204a0f2ec --- /dev/null +++ b/public/brca_aurora_2022/meta_clinical_sample.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: brca_aurora_2022 +genetic_alteration_type: CLINICAL +datatype: SAMPLE_ATTRIBUTES +data_filename: data_clinical_sample.txt diff --git a/public/brca_aurora_2022/meta_cna_hg38_seg.txt b/public/brca_aurora_2022/meta_cna_hg38_seg.txt new file mode 100644 index 0000000000..a2414caf2a --- /dev/null +++ b/public/brca_aurora_2022/meta_cna_hg38_seg.txt @@ -0,0 +1,6 @@ +cancer_study_identifier: brca_aurora_2022 +genetic_alteration_type: COPY_NUMBER_ALTERATION +datatype: SEG +reference_genome_id: hg38 +description: Segment data for the aurora cancer study +data_filename: data_cna_hg38.seg diff --git a/public/brca_aurora_2022/meta_log2_cna.txt b/public/brca_aurora_2022/meta_log2_cna.txt new file mode 100644 index 0000000000..ba952a93a2 --- /dev/null +++ b/public/brca_aurora_2022/meta_log2_cna.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: brca_aurora_2022 +genetic_alteration_type: COPY_NUMBER_ALTERATION +datatype: LOG2-VALUE +stable_id: log2CNA +show_profile_in_analysis_tab: false +profile_description: Log2 copy-number values for each gene +profile_name: Log2 copy-number values +data_filename: data_log2_cna.txt diff --git a/public/brca_aurora_2022/meta_methylation_hm450.txt b/public/brca_aurora_2022/meta_methylation_hm450.txt new file mode 100644 index 0000000000..b19f740e36 --- /dev/null +++ b/public/brca_aurora_2022/meta_methylation_hm450.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: brca_aurora_2022 +genetic_alteration_type: METHYLATION +datatype: CONTINUOUS +stable_id: methylation_hm450 +show_profile_in_analysis_tab: false +profile_name: Methylation (EPIC) +profile_description: Methylation beta-values +data_filename: data_methylation_hm450.txt diff --git a/public/brca_aurora_2022/meta_metsdx.txt b/public/brca_aurora_2022/meta_metsdx.txt new file mode 100644 index 0000000000..042505750a --- /dev/null +++ b/public/brca_aurora_2022/meta_metsdx.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: brca_aurora_us +genetic_alteration_type: CLINICAL +datatype: TIMELINE +data_filename: data_metsdx.txt diff --git a/public/brca_aurora_2022/meta_mrna_seq_rsem_zscores_ref_all_samples.txt b/public/brca_aurora_2022/meta_mrna_seq_rsem_zscores_ref_all_samples.txt new file mode 100644 index 0000000000..292da6f95c --- /dev/null +++ b/public/brca_aurora_2022/meta_mrna_seq_rsem_zscores_ref_all_samples.txt @@ -0,0 +1,8 @@ +cancer_study_identifier: brca_aurora_2022 +genetic_alteration_type: MRNA_EXPRESSION +datatype: Z-SCORE +stable_id: rna_seq_mrna_median_Zscores +show_profile_in_analysis_tab: true +profile_name: mRNA Expression z-Scores (RNA Seq V2 RSEM) +profile_description: mRNA z-Scores log2 transformed (RNA Seq V2 RSEM) +data_filename: data_mrna_seq_rsem_zscores_ref_all_samples.txt diff --git a/public/brca_aurora_2022/meta_mutations.txt b/public/brca_aurora_2022/meta_mutations.txt new file mode 100644 index 0000000000..dede2384a0 --- /dev/null +++ b/public/brca_aurora_2022/meta_mutations.txt @@ -0,0 +1,9 @@ +cancer_study_identifier: brca_aurora_2022 +genetic_alteration_type: MUTATION_EXTENDED +datatype: MAF +stable_id: mutations +show_profile_in_analysis_tab: true +profile_description: Mutation data from whole exome sequencing. +profile_name: Mutations +swissprot_identifier: accession +data_filename: data_mutations.txt diff --git a/public/brca_aurora_2022/meta_resource_definition.txt b/public/brca_aurora_2022/meta_resource_definition.txt new file mode 100644 index 0000000000..3cac01315d --- /dev/null +++ b/public/brca_aurora_2022/meta_resource_definition.txt @@ -0,0 +1,3 @@ +cancer_study_identifier: brca_aurora_us +resource_type: DEFINITION +data_filename: data_resource_definition.txt \ No newline at end of file diff --git a/public/brca_aurora_2022/meta_resource_sample.txt b/public/brca_aurora_2022/meta_resource_sample.txt new file mode 100644 index 0000000000..ec8e2fa0d8 --- /dev/null +++ b/public/brca_aurora_2022/meta_resource_sample.txt @@ -0,0 +1,3 @@ +cancer_study_identifier: brca_aurora_2022 +resource_type: SAMPLE +data_filename: data_resources_samples.txt diff --git a/public/brca_aurora_2022/meta_study.txt b/public/brca_aurora_2022/meta_study.txt new file mode 100644 index 0000000000..edde27401f --- /dev/null +++ b/public/brca_aurora_2022/meta_study.txt @@ -0,0 +1,7 @@ +type_of_cancer: brca +cancer_study_identifier: brca_aurora_2022 +name: Aurora-US Metastatic Breast Cancer +description: Retrospective Tissue Collection; an initiative of the Breast Cancer Research Foundation +groups: PUBLIC +reference_genome: hg38 +add_global_case_list: false diff --git a/public/brca_aurora_2022/meta_surgery.txt b/public/brca_aurora_2022/meta_surgery.txt new file mode 100644 index 0000000000..122e3f1382 --- /dev/null +++ b/public/brca_aurora_2022/meta_surgery.txt @@ -0,0 +1,4 @@ +cancer_study_identifier: brca_aurora_us +genetic_alteration_type: CLINICAL +datatype: TIMELINE +data_filename: data_surgery.txt