RT Journal Article
SR Electronic
T1 Fast gene set enrichment analysis
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 060012
DO 10.1101/060012
A1 Gennady Korotkevich
A1 Vladimir Sukhov
A1 Nikolay Budin
A1 Boris Shpak
A1 Maxim N. Artyomov
A1 Alexey Sergushichev
YR 2021
UL http://biorxiv.org/content/early/2021/02/01/060012.abstract
AB 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 even seconds. To confirm the accuracy of the method, we also developed an exact algorithm for GSEA P-values calculation for integer gene-level statistics. Using the exact algorithm as a reference we show that FGSEA is able to routinely estimate P-values up to 10−100 with a small and predictable estimation error. We systematically evaluate FGSEA on a collection of 605 datasets and show that FGSEA recovers much more statistically significant pathways compared to other implementations.FGSEA is open source and available as an R package in Bioconductor (http://bioconductor.org/packages/fgsea/) and on GitHub (https://github.com/ctlab/fgsea/).Competing Interest StatementThe authors have declared no competing interest.