FDR-FET: an optimizing gene set enrichment analysis method.

ABSTRACT: Gene set enrichment analysis for analyzing large profiling and screening experiments can reveal unifying biological schemes based on previously accumulated knowledge represented as "gene sets". Most of the existing implementations use a fixed fold-change or P value cutoff to generate regulated gene lists. However, the threshold selection in most cases is arbitrary, and has a significant effect on the test outcome and interpretation of the experiment. We developed a new gene set enrichment analysis method, ie, FDR-FET, which dynamically optimizes the threshold choice and improves the sensitivity and selectivity of gene set enrichment analysis. The procedure translates experimental results into a series of regulated gene lists at multiple false discovery rate (FDR) cutoffs, and computes the

SUBMITTER: Ji RR 

PROVIDER: S-EPMC3169954 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature