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On testing the significance of sets of genes. (English) Zbl 1129.62102
Summary: 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 A. Subramanian et al. [Proc. Natl. Acad. Sci. USA 102, 15545–15550 (2005)]. 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.

MSC:
62P10 Applications of statistics to biology and medical sciences; meta analysis
92C40 Biochemistry, molecular biology
92D10 Genetics and epigenetics
62-09 Graphical methods in statistics (MSC2010)
Software:
R; GSA
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