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PeerJ. 2016 Feb 16;3:e1499. doi: 10.7717/peerj.1499. eCollection 2015.

A pan-cancer analysis of prognostic genes.

Author information

1
Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States; omnesres.com, Charlottesville, United States.
2
Department of Biochemistry and Molecular Genetics, University of Virginia , Charlottesville, VA , United States.
3
Center for Public Health Genomics, University of Virginia, Charlottesville, VA, United States; Department of Public Health Sciences, Biostatistics Section, University of Virginia, Charlottesville, VA, United States.

Abstract

Numerous studies have identified prognostic genes in individual cancers, but a thorough pan-cancer analysis has not been performed. In addition, previous studies have mostly used microarray data instead of RNA-SEQ, and have not published comprehensive lists of associations with survival. Using recently available RNA-SEQ and clinical data from The Cancer Genome Atlas for 6,495 patients, we have investigated every annotated and expressed gene's association with survival across 16 cancer types. The most statistically significant harmful and protective genes were not shared across cancers, but were enriched in distinct gene sets which were shared across certain groups of cancers. These groups of cancers were independently recapitulated by both unsupervised clustering of Cox coefficients (a measure of association with survival) for individual genes, and for gene programs. This analysis has revealed unappreciated commonalities among cancers which may provide insights into cancer pathogenesis and rationales for co-opting treatments between cancers.

KEYWORDS:

Cancer; Cox; Pan-cancer; Prognostic; RNA-SEQ; Regression; TCGA; mRNA

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