Programs and Data Sets

The National Cancer Institute (NCI) Genomic Data Commons (GDC) and Proteomics Data Commons (PDC) provide the cancer research community with data repositories that enables data sharing across cancer genomic and proteomic studies (known as Programs) in support of precision medicine.

The ISB-CGC started with The Cancer Genome Atlas (TCGA) data sets but has expanded to include other data sets from programs such as Therapeutically Applicable Research To Generate Effective Treatments (TARGET). Along with the NCI GDC and PDC data sets, ISB-CGC hosts data sets from programs such as Catalogue Of Somatic Mutations In Cancer (COSMIC) from the Wellcome Trust Sanger Institute. We are always interested in adding new data sets, so if you have any suggestions or requests for additional data, please let us know (feedback@isb-cgc.org).

Clinical, Biospecimen and Processed -Omics Data Sets

From Genomic Data Commons

../_images/omicsData.png

Between ISB-CGC and the NCI GDC, there are many cancer data sets available on the Google Cloud Platform. ISB-CGC hosts some carefully curated, high-level clinical, biospecimen and molecular data sets and tables in Google BigQuery as well as radiology and pathology images in Google Cloud Storage. The GDC hosts several more data sets that include low-level sequencing data. For more information about the GDC, see the GDC Overview.

Clinical, biospecimen and processed -omics data (such as RNASeq, etc.) are available in the GDC Cloud Storage buckets, in ISB-CGC BigQuery tables and through ISB-CGC web tools. The table below lists each Program and where (through ISB-CGC) that you can find its data.

  • Within the detailed documentation on each Program (click on the Program name), there is an example of how to use the metadata stored in ISB-CGC BigQuery tables to locate the Program’s files on the GDC Google Cloud Storage buckets.
  • To learn more about using this data with ISB-CGC web tools, go to the ISB-CGC Web Interface section of this document.
  • To locate these tables in the ISB-CGC BigQuery project, use the ISB-CGC BigQuery Table Search.
Program GDC Google Cloud Storage ISB-CGC BigQuery Tables ISB-CGC Cohort Builder
BEATAML checkmark checkmark checkmark
CCLE checkmark checkmark checkmark
CGCI checkmark checkmark  
CMI checkmark checkmark  
CPTAC checkmark checkmark  
CTSP checkmark checkmark  
FM checkmark checkmark *  
GENIE checkmark checkmark *  
HCMI checkmark checkmark  
MMRF checkmark checkmark *  
NCICCR checkmark checkmark *  
OHSU checkmark checkmark *  
ORGANOID checkmark checkmark  
TARGET checkmark checkmark checkmark
TCGA checkmark checkmark checkmark
TCGA Pathology and Radiology images checkmark checkmark checkmark
VAREPOP checkmark checkmark *  
WCDT checkmark checkmark  

*Clinical and metadata only available

From Proteomics Data Commons

PDC protein expression data are available in ISB-CGC BigQuery tables. The table below lists each Program.

Program PDC AWS Cloud Storage ISB-CGC BigQuery Tables ISB-CGC Cohort Builder
CBTN   checkmark  
CPTAC   checkmark  
Georgetown Proteomics Research Program   checkmark  
ICPC   checkmark  
Quantitative Digital Maps of Tissue Biopsies   checkmark  

From Other Sources

Program GDC Google Cloud Storage ISB-CGC BigQuery Tables ISB-CGC Cohort Builder
COSMIC No, the COSMIC database is maintained by the Wellcome Sanger Institute, UK Yes, COSMIC data is in BigQuery for registered users. Learn more about how to gain access to the COSMIC data here  
Pan-Cancer Atlas   checkmark  

Reference Data Sets

ISB-CGC hosts reference tables in BigQuery with information that describes or annotates human or other genomes, or is necessary to work with data generated by specific platforms.

File Metadata Data Sets

ISB-CGC hosts metadata tables in BigQuery with information that points to the raw and processed cancer data in the NCI GDC Google Cloud Storage buckets.


Have feedback or corrections? Please email us at feedback@isb-cgc.org.