Clinical Proteomic Tumor Analysis Consortium 3 (CPTAC-3)

Stream data with DDA:

from dagshub.streaming import DagsHubFilesystem

fs = DagsHubFilesystem(".", repo_url="https://dagshub.com/DagsHub-Datasets/cptac-3-dataset")

fs.listdir("s3://gdc-cptac-phs001287-2-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-3 is the Phase III of the CPTAC Initiative. The dataset contains open RNA-Seq Gene 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-3 is the Phase III of the CPTAC Initiative. The dataset contains open RNA-Seq Gene 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
   • ARN: arn:aws:s3:::gdc-cptac-phs001287-2-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-3
   • 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: 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

2. publication:

   • 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