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cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018 |
stable_id: hnsc_tcga_pan_can_atlas_2018_rna_seq_v2_mrna |
case_list_name: Samples with mRNA data (RNA Seq V2) |
case_list_description: Samples with mRNA expression data (515 samples) |
case_list_category: all_cases_with_mrna_rnaseq_data |
case_list_ids: TCGA-CV-A45Q-01 TCGA-BA-5149-01 TCGA-CV-5966-01 TCGA-CR-6467-01 TCGA-T2-A6WX-01 TCGA-IQ-A61O-01 TCGA-CN-6998-01 TCGA-CN-6019-01 TCGA-UF-A7JJ-01 TCGA-CN-5366-01 TCGA-MT-A67A-01 TCGA-CX-7085-01 TCGA-CQ-6220-01 TCGA-CV-A45Y-01 TCGA-QK-A8ZB-01 TCGA-CQ-7071-01 TCGA-CN-5355-01 TCGA-CR-7377-01 TCGA-H7-8502-01 T... |
cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018 |
stable_id: hnsc_tcga_pan_can_atlas_2018_all |
case_list_name: All samples |
case_list_description: All samples (523 samples) |
case_list_category: all_cases_in_study |
case_list_ids: TCGA-CV-A45Q-01 TCGA-BA-5149-01 TCGA-CV-5966-01 TCGA-CR-6467-01 TCGA-T2-A6WX-01 TCGA-IQ-A61O-01 TCGA-CN-6998-01 TCGA-CN-6019-01 TCGA-UF-A7JJ-01 TCGA-CN-5366-01 TCGA-MT-A67A-01 TCGA-CX-7085-01 TCGA-CQ-6220-01 TCGA-CV-A45Y-01 TCGA-QK-A8ZB-01 TCGA-CQ-7071-01 TCGA-CN-5355-01 TCGA-CN-4726-01 TCGA-CR-5250-01 T... |
cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018 |
stable_id: hnsc_tcga_pan_can_atlas_2018_cna |
case_list_name: Samples with CNA data |
case_list_description: Samples with CNA data (517 samples) |
case_list_category: all_cases_with_cna_data |
case_list_ids: TCGA-CV-A45Q-01 TCGA-BA-5149-01 TCGA-CV-5966-01 TCGA-CR-6467-01 TCGA-T2-A6WX-01 TCGA-IQ-A61O-01 TCGA-CN-6998-01 TCGA-CN-6019-01 TCGA-UF-A7JJ-01 TCGA-CN-5366-01 TCGA-MT-A67A-01 TCGA-CX-7085-01 TCGA-CQ-6220-01 TCGA-CV-A45Y-01 TCGA-QK-A8ZB-01 TCGA-CQ-7071-01 TCGA-CN-5355-01 TCGA-CR-7377-01 TCGA-H7-8502-01 T... |
cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018 |
stable_id: hnsc_tcga_pan_can_atlas_2018_cnaseq |
case_list_name: Samples with mutation and CNA data |
case_list_description: Samples with mutation and CNA data (496 samples) |
case_list_category: all_cases_with_mutation_and_cna_data |
case_list_ids: TCGA-CV-A45Q-01 TCGA-BA-5149-01 TCGA-CV-5966-01 TCGA-CR-6467-01 TCGA-T2-A6WX-01 TCGA-IQ-A61O-01 TCGA-CN-6998-01 TCGA-CN-6019-01 TCGA-UF-A7JJ-01 TCGA-CN-5366-01 TCGA-MT-A67A-01 TCGA-CX-7085-01 TCGA-CQ-6220-01 TCGA-CV-A45Y-01 TCGA-QK-A8ZB-01 TCGA-CQ-7071-01 TCGA-CN-5355-01 TCGA-P3-A6T2-01 TCGA-CR-5250-01 T... |
cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018 |
stable_id: hnsc_tcga_pan_can_atlas_2018_3way_complete |
case_list_name: Complete samples |
case_list_description: Samples with mutation, CNA and expression data (488 samples) |
case_list_category: all_cases_with_mutation_and_cna_and_mrna_data |
case_list_ids: TCGA-CV-A45Q-01 TCGA-BA-5149-01 TCGA-CV-5966-01 TCGA-CR-6467-01 TCGA-T2-A6WX-01 TCGA-IQ-A61O-01 TCGA-CN-6998-01 TCGA-CN-6019-01 TCGA-UF-A7JJ-01 TCGA-CN-5366-01 TCGA-MT-A67A-01 TCGA-CX-7085-01 TCGA-CQ-6220-01 TCGA-CV-A45Y-01 TCGA-QK-A8ZB-01 TCGA-CQ-7071-01 TCGA-CN-5355-01 TCGA-P3-A6T2-01 TCGA-CR-5250-01 T... |
cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018 |
stable_id: hnsc_tcga_pan_can_atlas_2018_log2CNA |
case_list_name: Samples with log2 copy-number data |
case_list_description: Samples with log2 copy-number data (517 samples) |
case_list_category: all_cases_with_log2_cna_data |
case_list_ids: TCGA-CV-A45Q-01 TCGA-BA-5149-01 TCGA-CV-5966-01 TCGA-CR-6467-01 TCGA-T2-A6WX-01 TCGA-IQ-A61O-01 TCGA-CN-6998-01 TCGA-CN-6019-01 TCGA-UF-A7JJ-01 TCGA-CN-5366-01 TCGA-MT-A67A-01 TCGA-CX-7085-01 TCGA-CQ-6220-01 TCGA-CV-A45Y-01 TCGA-QK-A8ZB-01 TCGA-CQ-7071-01 TCGA-CN-5355-01 TCGA-CR-7377-01 TCGA-H7-8502-01 T... |
cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018 |
stable_id: hnsc_tcga_pan_can_atlas_2018_microbiome |
case_list_name: Samples with microbiome data |
case_list_description: All samples with microbiome data (514 samples) |
case_list_category: other |
case_list_ids: TCGA-CV-A45Q-01 TCGA-BA-5149-01 TCGA-UF-A7JJ-01 TCGA-CR-6467-01 TCGA-T2-A6WX-01 TCGA-IQ-A61O-01 TCGA-CN-6998-01 TCGA-CN-6019-01 TCGA-CV-5966-01 TCGA-CN-5366-01 TCGA-MT-A67A-01 TCGA-CX-7085-01 TCGA-CQ-6220-01 TCGA-CV-A45Y-01 TCGA-QK-A8ZB-01 TCGA-CQ-7071-01 TCGA-CN-5355-01 TCGA-P3-A6T2-01 TCGA-CR-5250-01 T... |
cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018 |
stable_id: hnsc_tcga_pan_can_atlas_2018_rppa |
case_list_name: Samples with protein data (RPPA) |
case_list_description: Samples with protein data (RPPA) (211 samples) |
case_list_category: all_cases_with_rppa_data |
case_list_ids: TCGA-CN-4730-01 TCGA-BA-5149-01 TCGA-CV-5436-01 TCGA-CV-5966-01 TCGA-CV-6436-01 TCGA-CV-7418-01 TCGA-CN-6998-01 TCGA-CV-5443-01 TCGA-CV-7263-01 TCGA-CV-7103-01 TCGA-CN-6019-01 TCGA-CN-4741-01 TCGA-CX-7219-01 TCGA-CN-4731-01 TCGA-CN-5366-01 TCGA-CV-6956-01 TCGA-CN-5369-01 TCGA-CV-7100-01 TCGA-BA-6869-01 T... |
cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018 |
stable_id: hnsc_tcga_pan_can_atlas_2018_sequenced |
case_list_name: Samples with mutation data |
case_list_description: Samples with mutation data (515 samples) |
case_list_category: all_cases_with_mutation_data |
case_list_ids: TCGA-CV-A45Q-01 TCGA-BA-5149-01 TCGA-CV-5966-01 TCGA-CR-6467-01 TCGA-T2-A6WX-01 TCGA-IQ-A61O-01 TCGA-CN-6998-01 TCGA-CN-6019-01 TCGA-UF-A7JJ-01 TCGA-CN-5366-01 TCGA-MT-A67A-01 TCGA-CX-7085-01 TCGA-CQ-6220-01 TCGA-CV-A45Y-01 TCGA-QK-A8ZB-01 TCGA-CQ-7071-01 TCGA-CN-5355-01 TCGA-P3-A6T2-01 TCGA-CR-5250-01 T... |
cancer_study_identifier: hnsc_tcga_pan_can_atlas_2018 |
stable_id: hnsc_tcga_pan_can_atlas_2018_sv |
case_list_name: Samples with SV data |
case_list_description: All samples (515 samples) |
case_list_category: all_cases_with_sv_data |
case_list_ids: TCGA-CV-A45Q-01 TCGA-BA-5149-01 TCGA-CV-5966-01 TCGA-CR-6467-01 TCGA-T2-A6WX-01 TCGA-IQ-A61O-01 TCGA-CN-6998-01 TCGA-CN-6019-01 TCGA-UF-A7JJ-01 TCGA-CN-5366-01 TCGA-MT-A67A-01 TCGA-CX-7085-01 TCGA-CQ-6220-01 TCGA-CV-A45Y-01 TCGA-QK-A8ZB-01 TCGA-CQ-7071-01 TCGA-CN-5355-01 TCGA-P3-A6T2-01 TCGA-CR-5250-01 T... |
ENTITY_STABLE_ID NAME DESCRIPTION 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-6872-0... |
1p_status 1p Copy number status of 1p Unchanged Unchanged Unchanged NA Gain Unchanged NA Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged NA Unchanged Loss Loss Unchanged Unchanged NA Unchanged Unchanged Unchanged Unchanged Loss Unchanged NA Unchanged NA Unchanged Unchanged NA Unchanged Loss Unchanged Unchan... |
1q_status 1q Copy number status of 1q Unchanged Unchanged Unchanged Unchanged Loss Unchanged Loss Unchanged Gain Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Gain Gain NA Loss Gain NA Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged L... |
2p_status 2p Copy number status of 2p Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Gain Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Loss Unchanged Gain Unchanged Unchanged NA NA Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged U... |
2q_status 2q Copy number status of 2q Unchanged Unchanged NA Unchanged Unchanged Unchanged NA Unchanged Unchanged Unchanged Unchanged NA Unchanged Unchanged Unchanged Unchanged NA Unchanged Loss Unchanged Gain NA Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged NA Unchanged Unchanged Unchanged NA Unchanged N... |
3p_status 3p Copy number status of 3p Loss Loss Loss Loss Loss Unchanged Unchanged NA Loss Unchanged NA Loss Unchanged Loss Loss Loss Loss Loss Unchanged NA Loss Unchanged Unchanged Loss Loss NA Loss NA Loss Unchanged Unchanged Loss Unchanged Loss Loss Unchanged Unchanged Loss Gain Loss NA Unchanged Loss Unchanged NA N... |
3q_status 3q Copy number status of 3q Unchanged Unchanged Gain Gain Gain Gain Unchanged Gain NA Unchanged Gain Gain Gain Gain NA Gain NA Gain NA Gain Gain Gain Gain Gain Gain NA Unchanged Gain Unchanged Unchanged NA Gain Unchanged NA Gain Unchanged Gain Gain Gain Gain Unchanged NA Unchanged Unchanged Gain Unchanged Los... |
4p_status 4p Copy number status of 4p Unchanged Loss Loss Loss Loss NA Unchanged Unchanged Loss Unchanged NA NA Unchanged NA Unchanged Loss Loss Gain NA Gain Unchanged NA Unchanged NA Loss Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Loss Loss Unchanged NA Loss Gain NA Unchanged Loss ... |
4q_status 4q Copy number status of 4q Unchanged Unchanged Unchanged Loss Unchanged Unchanged Unchanged Unchanged Loss Unchanged NA NA Unchanged Unchanged Unchanged Loss Unchanged NA Loss NA Loss NA Unchanged Unchanged NA Unchanged Loss Unchanged Unchanged Unchanged Unchanged NA Unchanged Loss NA Unchanged Unchanged Unc... |
5p_status 5p Copy number status of 5p Gain Gain NA Gain Unchanged Unchanged Unchanged Unchanged Gain Unchanged Unchanged Gain Gain Gain Gain NA NA Gain Gain Gain Gain Unchanged Unchanged Unchanged Gain NA Gain Unchanged Unchanged Unchanged Unchanged Gain Unchanged Unchanged NA Gain Gain Gain Unchanged Gain NA Gain Unch... |
5q_status 5q Copy number status of 5q Unchanged Loss Unchanged Loss Unchanged Unchanged Unchanged Unchanged Loss Unchanged Unchanged Unchanged Unchanged NA Unchanged Loss NA NA Loss Loss Gain Loss Unchanged Unchanged Loss Unchanged Loss Unchanged Loss Unchanged Unchanged Loss Unchanged Loss Loss Unchanged Gain Loss Unc... |
6p_status 6p Copy number status of 6p NA Unchanged Unchanged Unchanged NA Unchanged Loss Unchanged Gain Unchanged Unchanged Unchanged Unchanged NA NA Unchanged Unchanged Unchanged Unchanged Unchanged Gain Unchanged Unchanged NA Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Lo... |
6q_status 6q Copy number status of 6q Unchanged Unchanged NA Unchanged Unchanged Unchanged Loss Unchanged Loss Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Loss Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged Unch... |
7p_status 7p Copy number status of 7p Unchanged Gain Gain Unchanged Gain Unchanged Unchanged NA Gain Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged NA Unchanged NA Loss NA Unchanged Loss Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged NA Unchanged Unchanged Unchanged Unchanged Gain Unchanged Un... |
7q_status 7q Copy number status of 7q Unchanged Loss Loss Unchanged Unchanged Unchanged Loss Unchanged Unchanged Unchanged Unchanged Unchanged Unchanged NA Unchanged Unchanged Unchanged NA Loss NA Unchanged NA Loss Unchanged Unchanged Unchanged Unchanged Unchanged NA Unchanged Unchanged NA Unchanged Loss NA Unchanged U... |
8p_status 8p Copy number status of 8p Loss Loss Loss Unchanged Loss Loss NA Unchanged Unchanged Unchanged Loss Loss Gain Loss Unchanged Loss Gain Loss Loss Loss Unchanged Unchanged Unchanged Loss Loss Unchanged Loss NA NA Unchanged Unchanged Loss Unchanged Unchanged Loss Gain Gain Loss Gain Loss NA Gain Loss Loss Gain ... |
8q_status 8q Copy number status of 8q Gain Unchanged NA Unchanged Gain NA Gain Unchanged Gain Unchanged Gain Gain Gain NA Unchanged Gain Gain Gain Gain Gain NA Gain Unchanged Gain NA Gain Unchanged Gain NA Gain Gain Gain NA Unchanged Gain Gain Gain Gain Gain Gain Gain Unchanged Unchanged Gain Gain Unchanged Gain Unchan... |
9p_status 9p Copy number status of 9p Unchanged Loss Loss Loss Loss Unchanged Unchanged Unchanged Loss Gain Unchanged Unchanged Gain Loss NA Loss Loss NA Unchanged Loss Loss Unchanged Unchanged Loss Loss Gain Loss Loss Loss Unchanged Gain Unchanged Gain Loss Loss Unchanged Unchanged Loss Unchanged Unchanged Unchanged U... |
9q_status 9q Copy number status of 9q NA NA Unchanged Unchanged Gain Unchanged Unchanged Unchanged Gain Gain Unchanged Unchanged Gain Unchanged Unchanged NA Loss Unchanged Unchanged Loss Unchanged Unchanged Unchanged Unchanged Unchanged Gain Unchanged Gain Unchanged Unchanged Unchanged Unchanged Gain NA Unchanged Uncha... |
10p_status 10p Copy number status of 10p Unchanged Unchanged NA Loss Unchanged Gain Unchanged Unchanged Gain Unchanged Unchanged Unchanged Unchanged Loss Gain Loss Unchanged Unchanged Loss Loss Unchanged Unchanged Unchanged NA NA Unchanged Loss Unchanged Unchanged Unchanged Unchanged Loss Unchanged Unchanged Loss Uncha... |
10q_status 10q Copy number status of 10q Unchanged Loss Unchanged Loss Unchanged Gain Loss Unchanged Loss Unchanged Unchanged Unchanged Unchanged NA NA NA Unchanged NA Unchanged Unchanged Gain NA Unchanged Unchanged Loss Unchanged Unchanged Unchanged Loss Unchanged Unchanged Loss Unchanged Unchanged Loss Unchanged Unch... |
11p_status 11p Copy number status of 11p Unchanged Unchanged Unchanged NA Unchanged Unchanged Unchanged Unchanged NA Gain Unchanged Unchanged Unchanged NA Unchanged Loss Loss Loss NA Loss Unchanged Loss Unchanged Loss NA Unchanged Unchanged Loss Unchanged Unchanged Unchanged Unchanged Unchanged Loss NA Unchanged Unchan... |
11q_status 11q Copy number status of 11q Unchanged Loss Loss Loss Loss Unchanged Unchanged NA NA Gain Unchanged Gain NA Loss Unchanged NA Loss Loss Loss Loss Unchanged NA Loss Loss Unchanged Loss Unchanged Loss Unchanged Unchanged Loss Unchanged Unchanged NA Gain Unchanged NA Unchanged Gain NA NA NA Unchanged Unchanged... |
12p_status 12p Copy number status of 12p Unchanged Unchanged Unchanged Unchanged Loss Unchanged Unchanged Unchanged Gain Unchanged Unchanged Unchanged Gain NA Unchanged NA NA Loss NA Unchanged Gain NA NA Unchanged Unchanged Unchanged Unchanged Unchanged Loss Unchanged Gain Unchanged Unchanged NA Gain Unchanged Gain Gai... |
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Check out the documentation for more information.
Improving PanCancer Atlas Data: (transformation steps for the new data types being added)
The Timeline/Treatment data:
Data Source
- GDAC Firehose: https://gdac.broadinstitute.org/
- File Used:
Merge_Clinical.Level_1.20160128(clin.merged.txt) for each cancer type.
Data Transformation
- The detailed transformation steps are listed in the Pull Request here
The Genetic Ancestry data:
Data Source
- GDAC Firehose: https://gdc.cancer.gov/about-data/publications/CCG-AIM-2020
- File Used:
Admixture_by_sample.txt(Admix percent by sample) for each cancer type.
The Methylation data:
Data Source
- GDAC Firehose: https://gdc.cancer.gov/node/977
- File Used:
jhu-usc.edu_PANCAN_HumanMethylation450.betaValue_whitelisted.tsv(DNA methylation 450K only beta value data matrix) for each cancer type.
Data Transformation
- The detailed transformation steps are listed in the Pull Request here
- The meta info for the Infinium Illumina 450k probes used for this profile is under the folder "probe_meta" "probe_450k_mapinfo_PQ.txt" is the original download from Illumina.
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