Patient-oriented gene set analysis for cancer mutation dataReport as inadecuate

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Genome Biology

, 11:R112

First Online: 23 November 2010Received: 09 May 2010Revised: 26 August 2010Accepted: 23 November 2010


Recent research has revealed complex heterogeneous genomic landscapes in human cancers. However, mutations tend to occur within a core group of pathways and biological processes that can be grouped into gene sets. To better understand the significance of these pathways, we have developed an approach that initially scores each gene set at the patient rather than the gene level. In mutation analysis, these patient-oriented methods are more transparent, interpretable, and statistically powerful than traditional gene-oriented methods.

AbbreviationsCaMP scorecancer mutation prevalence score

CAN-genecandidate cancer gene

CAT plot-correspondence at the top- plot

FDRfalse discovery rate

GBMglioblastoma multiforme

LRTlikelihood ratio test.

Electronic supplementary materialThe online version of this article doi:10.1186-gb-2010-11-11-r112 contains supplementary material, which is available to authorized users.

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Author: Simina M Boca - Kenneth W Kinzler - Victor E Velculescu - Bert Vogelstein - Giovanni Parmigiani


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