biostudies-literatureTamayo PNICHD NIH HHSNCI NIH HHS472-87https://www.ebi.ac.uk/biostudies/studies/S-EPMC3758419biostudies-literatureUnknown25(1)Since its first publication in 2003, the Gene Set Enrichment Analysis method, based on the Kolmogorov-Smirnov statistic, has been heavily used, modified, and also questioned. Recently a simplified approach using a one-sample t-test score to assess enrichment and ignoring gene-gene correlations was proposed by Irizarry et al. 2009 as a serious contender. The argument criticizes Gene Set Enrichment Analysis's nonparametric nature and its use of an empirical null distribution as unnecessary and hard to compute. We refute these claims by careful consideration of the assumptions of the simplified method and its results, including a comparison with Gene Set Enrichment Analysis's on a large benchmark set of 50 datasets. Our results provide strong empirical evidence that gene-gene correlations canStatistical methods in medical researchThe limitations of simple gene set enrichment analysis assuming gene independence.PMC3758419R01 CA109467R01-CA121941P30 CA023100R01 CA121941U54 HD090255U24 CA194107Liberzon ATamayo PMesirov JPSteinhardt GfalseThe limitations of simple gene set enrichment analysis assuming gene independence.Since its first publication in 2003, the Gene Set Enrichment Analysis method, based on the Kolmogorov-Smirnov statistic, has been heavily used, modified, and also questioned. Recently a simplified approach using a one-sample t-test score to assess enrichment and ignoring gene-gene correlations was proposed by Irizarry et al. 2009 as a serious contender. The argument criticizes Gene Set Enrichment Analysis's nonparametric nature and its use of an empirical null distribution as unnecessary and hard to compute. We refute these claims by careful consideration of the assumptions of the simplified method and its results, including a comparison with Gene Set Enrichment Analysis's on a large benchmark set of 50 datasets. Our results provide strong empirical evidence that gene-gene correlations can2016-01-01T00:00:00Z2016 Feb2025-04-26T06:09:27.662Z2019-03-27T01:15:20ZS-EPMC37584192307059210.1177/0962280212460441