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June 2007 On testing the significance of sets of genes
Bradley Efron, Robert Tibshirani
Ann. Appl. Stat. 1(1): 107-129 (June 2007). DOI: 10.1214/07-AOAS101


This paper discusses the problem of identifying differentially expressed groups of genes from a microarray experiment. The groups of genes are externally defined, for example, sets of gene pathways derived from biological databases. Our starting point is the interesting Gene Set Enrichment Analysis (GSEA) procedure of Subramanian et al. [Proc. Natl. Acad. Sci. USA 102 (2005) 15545–15550]. We study the problem in some generality and propose two potential improvements to GSEA: the maxmean statistic for summarizing gene-sets, and restandardization for more accurate inferences. We discuss a variety of examples and extensions, including the use of gene-set scores for class predictions. We also describe a new R language package GSA that implements our ideas.


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Bradley Efron. Robert Tibshirani. "On testing the significance of sets of genes." Ann. Appl. Stat. 1 (1) 107 - 129, June 2007.


Published: June 2007
First available in Project Euclid: 29 June 2007

zbMATH: 1129.62102
MathSciNet: MR2393843
Digital Object Identifier: 10.1214/07-AOAS101

Keywords: gene set enrichment , Hypothesis testing , multiple testing

Rights: Copyright © 2007 Institute of Mathematical Statistics


Vol.1 • No. 1 • June 2007
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