cptac-2.yaml

Name: Clinical Proteomic Tumor Analysis Consortium 2 (CPTAC-2)
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-2 is the Phase II of the CPTAC Initiative (2011-2016).
  Datasets contain open RNA-Seq Gene Expression Quantification, miRNA-Seq Isoform Expression
  Quantification, and miRNA Expression Quantification data.
Documentation: https://cptac-data-portal.georgetown.edu/cptac/public?scope=Phase+II+%2525
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, miRNA-Seq Isoform Expression Quantification, miRNA-Seq
      miRNA Expression Quantification
    ARN: arn:aws:s3:::gdc-cptac-2-phs000892-2-open
    Region: us-east-1
    Type: S3 Bucket
DataAtWork:
  Tools & Applications:
    - Title: Genomic Data Commons
      URL: https://portal.gdc.cancer.gov/projects/CPTAC-2
      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: Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer
      URL: https://doi.org/10.1016/j.cell.2016.05.069
      AuthorName: |
        Hui Zhang, Tao Liu, Zhen Zhang, Samuel H. Payne, Bai Zhang, Jason E. McDermott, Jian-Ying
        Zhou, Vladislav A. Petyuk, Li Chen, Debjit Ray, Shisheng Sun, Feng Yang, Lijun Chen, Jing
        Wang, Punit Shah, Seong Won Cha, Paul Aiyetan, Sunghee Woo, Yuan Tian, Marina A. Gritsenko,
        Therese R. Clauss, Caitlin Choi, Matthew E. Monroe, Stefani Thomas, Song Nie, Chaochao Wu,
        Ronald J. Moore, Kun-Hsing Yu, David L. Tabb, David Fenyö, Vineet Bafna, Yue Wang, Henry
        Rodriguez, Emily S. Boja, Tara Hiltke, Robert C. Rivers, Lori Sokoll, Heng Zhu, Ie-Ming
        Shih, Leslie Cope, Akhilesh Pandey, Bing Zhang, Michael P. Snyder, Douglas A. Levine,
        Richard D. Smith, Daniel W. Chan, Karin D. Rodland, the CPTAC Investigators
    - Title: Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities
      URL: https://doi.org/10.1016/j.cell.2019.03.030
      AuthorName: |
        Suhas Vasaikar, Chen Huang, Xiaojing Wang. Vladislav A. Petyuk, Sara R. Savage, Bo Wen,
        Yongchao Dou, Yun Zhang, Zhiao Shi, Osama A. Arshad, Marina A. Gritsenko, Lisa J. Zimmerman,
        Jason E. McDermott, Therese R. Clauss, Ronald J. Moore, Rui Zhao, Matthew E. Monroe, Yi-Ting
        Wang, Matthew C. Chambers, Robbert J.C. Slebos, Ken S. Lau, Qianxing Mo, Li Ding, Matthew
        Ellis, Mathangi Thiagarajan, Christopher R. Kinsinger, Henry Rodriguez, Richard D. Smith,
        Karin D. Rodland, Daniel C. Liebler, Tao Liu, Bing Zhang, Clinical Proteomic Tumor Analysis
        Consortium
    - Title: |
        Proteomic analysis of colon and rectal carcinoma using standard and customized databases
      URL: https://doi.org/10.1038/sdata.2015.22
      AuthorName: Slebos RJ, Wang X, Wang X, Zhang B, Tabb DL, Liebler DC