PT  - JOURNAL ARTICLE
AU  - Alexey A. Sergushichev
TI  - An algorithm for fast preranked gene set enrichment analysis using cumulative statistic calculation
AID  - 10.1101/060012
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 060012
4099  - http://biorxiv.org/content/early/2016/06/20/060012.short
4100  - http://biorxiv.org/content/early/2016/06/20/060012.full
AB  - Gene set enrichment analysis is a widely used tool for analyzing gene expression data. However, current implementations are slow due to a large number of required samples for the analysis to have a good statistical power. In this paper we present a novel algorithm, that efficiently reuses one sample multiple times and thus speeds up the analysis. We show that it is possible to make hundreds of thousands permutations in a few minutes, which leads to very accurate p-values. This, in turn, allows applying standard FDR correction procedures, which are more accurate than the ones currently used. The method is implemented in a form of an R package and is freely available at https://github.com/ctlab/fgsea.