期刊
ANNALS OF APPLIED STATISTICS
卷 1, 期 1, 页码 107-129出版社
INST MATHEMATICAL STATISTICS
DOI: 10.1214/07-AOAS101
关键词
Multiple testing; gene set enrichment; hypothesis testing
资金
- NSF [DMS-05-05673, DMS-99-71405]
- National Institutes of Health [8RO1 EB002784, N01-HV-28183]
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 predictions. We also describe a new R language package GSA that implements our ideas.
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