On testing the significance of sets of genes
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Publication:995734
DOI10.1214/07-AOAS101zbMATH Open1129.62102arXivmath/0610667OpenAlexW2020859582MaRDI QIDQ995734FDOQ995734
Authors: Robert Tibshirani, Bradley Efron 
Publication date: 10 September 2007
Published in: The Annals of Applied Statistics (Search for Journal in Brave)
Abstract: 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.
Full work available at URL: https://arxiv.org/abs/math/0610667
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Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40) Genetics and epigenetics (92D10) Graphical methods in statistics (62A09)
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- Rotation testing in gene set enrichment analysis for small direct comparison experiments
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- Bayesian gene set analysis for identifying significant biological pathways
- A statistical framework for testing functional categories in microarray data
- Statistical tests for the intersection of independent lists of genes: sensitivity, FDR, and type I error control
- Invisible fence methods and the identification of differentially expressed gene sets
- Consistency of invariance-based randomization tests
- Robust \(U\)-type test for high dimensional regression coefficients using refitted cross-validation variance estimation
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