Fast gene set enrichment analysis

Gennady Korotkevich; Vladimir Sukhov; Alexey Sergushichev

doi:10.1101/060012

Abstract

Preranked gene set enrichment analysis (GSEA) is a widely used method for interpretation of gene expression data in terms of biological processes. Here we present FGSEA method that is able to estimate arbitrarily low GSEA P-values with a higher accuracy and much faster compared to other implementations. We also present a polynomial algorithm to calculate GSEA P-values exactly, which we use to practically confirm the accuracy of the method.

Footnotes

FGSEA-multilevel procedure has been added to estimate arbitrarily low P-values.

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