The Cancer Genome Atlas Clinical Explorer: An Interface for Identifying Clinical–Genomic Driver Associations

Version 2.0

What Genes are associated with a Clinical Parameter of your interest? These genes are identified by Elastic-net analysis.

Check if Gene/Protein/miR of your interest is associated with Clinical Parameters

Target:   Gene    Protein    miR  

What Cancer Type are you interested in?

What Clinical Parameter are you interested in?

Query by Gene, miR, or Protein by Cancer Type and Clinical Parameter
(Ex: Genetic profiles of TP53 in Colorectal cancer by MSI status)

Target:   Gene    Protein    miR

Two-hit hypothesis test
(Ex: Mutation counts for TP53 and WRN from COADREAD)

Target:   Gene   Protein   miR
Target:   Gene    miR
  • What are clinically relevant genes?
  • For instance, clinical stage associated genes are the ones having different mutation profiles between different stages. If a gene is mutated across all stages, it is not regarded as associated with clinical stage. For further explanation, look at our publication.

  • Navigate TCGA data 3 ways
  • Top panel: Search by -

    • clinically relevant Gene/miR/Protein
    • cancer type
    • clinical parameter

    Middle panel: Genetic profiling by clinical parameters

    Bottom panel: Testing two hit hypothesis. Search by Target/Genomic Pairs

  • Example queries
  • What genes are associated with clinical stage of colorectal cancer?

    What clinical parameters are associated with APC genes?

    How does PIK3CA behave differently between EBV infected and non-infected samples from the stomach?

    What is the difference in copy number changes of TP53 between samples with and without TP53 mutation?

Broad Firehose Version: 2015-04-02