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Fast gene set enrichment analysis

Gennady Korotkevich, Vladimir Sukhov, Alexey Sergushichev
doi: https://doi.org/10.1101/060012
Gennady Korotkevich
1Computer Technologies Laboratory, ITMO University, Saint Petersburg, 197101, Russia
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Vladimir Sukhov
1Computer Technologies Laboratory, ITMO University, Saint Petersburg, 197101, Russia
2JetBrains Research, Saint Petersburg, Russia
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Alexey Sergushichev
1Computer Technologies Laboratory, ITMO University, Saint Petersburg, 197101, Russia
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  • For correspondence: alserg@itmo.ru
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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.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 22, 2019.
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Fast gene set enrichment analysis
Gennady Korotkevich, Vladimir Sukhov, Alexey Sergushichev
bioRxiv 060012; doi: https://doi.org/10.1101/060012
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Fast gene set enrichment analysis
Gennady Korotkevich, Vladimir Sukhov, Alexey Sergushichev
bioRxiv 060012; doi: https://doi.org/10.1101/060012

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