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
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)
Two-hit hypothesis test
(Ex: Mutation counts for TP53 and WRN from COADREAD)
- What are clinically relevant genes?
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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
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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
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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