Fast gene set enrichment analysis

Abstract Gene set enrichment analysis (GSEA) is an ubiquitously used tool for evaluating pathway enrichment in transcriptional data. Typical experimental design consists in comparing two conditions with several replicates using a differential gene expression test followed by preranked GSEA performed against a collection of hundreds and thousands of pathways. However, the reference implementation of this method cannot accurately estimate small P-values, which significantly limits its sensitivity due to multiple hypotheses correction procedure. Here we present FGSEA (Fast Gene Set Enrichment Analysis) method that is able to estimate arbitrarily low GSEA P-values with a high accuracy in a matter of minutes or…