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  • Debarka Sengupta

Resources a bioinformatician, working on cancers should be aware of

Updated: Mar 27

Here we catalog SIX essential resources for bioinformatics research in the field of cancer.


cBioPortal: Pre-processed cancer omics data

  • Processed genotype and expression data from across hundreds of studies.

  • Data across studies are uniformly structured.

  • All pertinent clinical information is available.

  • To our knowledge, by far, the best resource for cancer informatics researchers.

  • It encompasses all consortia scale data such as TCGA.

  • Here is the link: https://www.cbioportal.org/.

  • Note that cBioPortal presents the variant calls as-is from the respective study. So if the study has matched normal samples, you can trust the somatic variant calls. So one has to be watchful.


genomAD: Processed exome and genome sequence data

  • 125,748 exomes and 15,708 genome sequences from various disease-specific and population genetic studies

  • The data is powerful since the consortium used joint variant calling

  • Helpful to control for polymorphisms

  • Here is the link: https://gnomad.broadinstitute.org/about


COSMIC


GEPIA

  • One-stop-shop for cancer (from TCGA) and normal (from GTEx) gene expression data.

  • The server allows all possible ways of comparing gene expression differences across cancer and healthy tissues.

  • Here is the link: http://gepia.cancer-pku.cn/


Cancer Dependency Map

Image credit: https://depmap.org/portal/

  • Excellent resource combining genome-wide loss of function screens using CRISPR/shRNA, omic data of established cancer cell lines, drug sensitivity data.

  • An excellent resource for AI-based precision oncology research.

  • Here is the link: https://depmap.org/portal/


CancerSCEM

#cancer #mutation #bioinformatics

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