Clinical Proteomic Tumor Analysis Consortium 2 (CPTAC-2)

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/cptac-2-dataset")

fs.listdir("s3://gdc-cptac-2-phs000892-2-open")

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.

Contact:

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.

Update Frequency:

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.

Managed By:

https://ctds.uchicago.edu/

Resources:

1. resource:

   • 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

Tags:

aws-pds, cancer, genomic, life sciences, transcriptomics, STRIDES

Tools & Applications:

1. tools & applications:

   • Title: Genomic Data Commons
   • URL: https://portal.gdc.cancer.gov/projects/CPTAC-2
   • AuthorName: National Cancer Institute
   • AuthorURL: https://gdc.cancer.gov/

2. tools & applications:

   • Title: Proteomic Data Commons
   • URL: https://pdc.esacinc.com/pdc/browse
   • AuthorName: National Cancer Institute
   • AuthorURL: https://pdc.esacinc.com/pdc

3. tools & applications:

   • Title: CPTAC Data Portal
   • URL: https://proteomics.cancer.gov/data-portal
   • AuthorName: National Cancer Institute
   • AuthorURL: https://proteomics.cancer.gov/

4. tools & applications:

   • Title: Cancer Genomics Cloud
   • URL: https://cgc-accounts.sbgenomics.com/
   • AuthorName: Seven Bridges
   • AuthorURL: http://www.cancergenomicscloud.org/

Publication:

1. publication:

   • 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

2. publication:

   • 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

3. publication:

   • 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