cptac-3.yaml

Name: Clinical Proteomic Tumor Analysis Consortium 3 (CPTAC-3)
Description: |
  The Clinical Proteomic Tumor Analysis Consortium (CPTAC) is a national effort to accelerate the
  understanding of the molecular basis of cancer through the application of large-scale proteome and
  genome analysis, or proteogenomics. CPTAC-3 is the Phase III of the CPTAC Initiative. The dataset
  contains open RNA-Seq Gene Expression Quantification data.
Documentation: https://cptac-data-portal.georgetown.edu/cptac/public?scope=Phase+III
Contact: dcf-support@datacommons.io
ManagedBy: "[Center for Translational Data Science at The University of Chicago](https://ctds.uchicago.edu/)"
UpdateFrequency: |
  Genomic Data Commons (GDC) is source of truth for this dataset; GDC offers monthly data releases,
  although this dataset may not be updated at every release.
Tags:
  - aws-pds
  - cancer
  - genomic
  - life sciences
  - transcriptomics
  - STRIDES
License: "NIH Genomic Data Sharing Policy: https://gdc.cancer.gov/access-data/data-access-policies"
Resources:
  - Description: RNA-Seq Gene Expression Quantification
    ARN: arn:aws:s3:::gdc-cptac-phs001287-2-open
    Region: us-east-1
    Type: S3 Bucket
DataAtWork:
  Tools & Applications:
    - Title: Genomic Data Commons
      URL: https://portal.gdc.cancer.gov/projects/CPTAC-3
      AuthorName: National Cancer Institute
      AuthorURL: https://gdc.cancer.gov/
    - Title: Proteomic Data Commons
      URL: https://pdc.esacinc.com/pdc/browse
      AuthorName: National Cancer Institute
      AuthorURL: https://pdc.esacinc.com/pdc
    - Title: CPTAC Data Portal
      URL: https://proteomics.cancer.gov/data-portal
      AuthorName: National Cancer Institute
      AuthorURL: https://proteomics.cancer.gov/
    - Title: Cancer Genomics Cloud
      URL: https://cgc-accounts.sbgenomics.com/
      AuthorName: Seven Bridges
      AuthorURL: http://www.cancergenomicscloud.org/
  Publications:
    - Title: Evaluation of NCI-7 Cell Line Panel as a Reference Material for Clinical Proteomics
      URL: https://www.ncbi.nlm.nih.gov/pubmed/29718670
      AuthorName: |
        Clark DJ, Hu Y, Bocik W, Chen L, Schnaubelt M, Roberts R, Shah P, Whiteley G, Zhang H
    - Title: Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma
      URL: https://doi.org/10.1016/j.cell.2019.10.007
      AuthorName: |
        Clark DJ, Dhanasekaran SM, Petralia F, Pan J, Song X, Hu Y, da Veiga Leprevost F, Reva B,
        Lih TM, Chang HY, Ma W, Huang C, Ricketts CJ, Chen L1, Krek A, Li Y, Rykunov D, Li QK, Chen
        LS, Ozbek U, Vasaikar S, Wu Y, Yoo S, Chowdhury S, Wyczalkowski MA, Ji J, Schnaubelt M, Kong
        A, Sethuraman S, Avtonomov DM, Ao M, Colaprico A, Cao S, Cho KC, Kalayci S, Ma S, Liu W,
        Ruggles K, Calinawan A, Gümüş ZH, Geizler D, Kawaler E, Teo GC, Wen B, Zhang Y, Keegan S, Li
        K, Chen F, Edwards N, Pierorazio PM, Chen XS, Pavlovich CP, Hakimi AA, Brominski G, Hsieh
        JJ, Antczak A, Omelchenko T, Lubinski J, Wiznerowicz M, Linehan WM, Kinsinger CR,
        Thiagarajan M, Boja ES, Mesri M, Hiltke T, Robles AI, Rodriguez H, Qian J, Fenyö D, Zhang B,
        Ding L, Schadt E, Chinnaiyan AM, Zhang Z, Omenn GS, Cieslik M, Chan DW, Nesvizhskii AI, Wang
        P, Zhang H; Clinical Proteomic Tumor Analysis Consortium