Skip to content

Gene set enrichment analysis

Gene Set Enrichment Analysis

Data Type

Gene set enrichment analysis is performed to summarize the biological pathways which are commonly enriched or depleted in a collection of differentially expressed genes. The collections of genes which have been annotated by biological pathways can be found in the MSigDB. The Bioconductor package used to perform GSEA is fgsea.

The output of this analysis is a table indicating the enrichment scores associated with each of the hallmark gene sets in the MSigDB.

User Guide

Parameters:

  • Gene Ranking Table: The input table must contain a ranking of genes by their enrichment score, with values for both gene score and p-value
  • Gene ID Column Name: Indiciate the name of the column in the Gene Ranking Table which contains the Gene ID
  • Gene Score Column Name: Indiciate the name of the column in the Gene Ranking Table which contains the Gene Score
  • P-Value Column Name: Indiciate the name of the column in the Gene Ranking Table which contains the P-Value

Workflow Repository: github.com/FredHutch/pw-gene-set-enrichment

Citations:

  • fgsea: Korotkevich G, Sukhov V, Sergushichev A (2019). “Fast gene set enrichment analysis.” bioRxiv. doi: 10.1101/060012, http://biorxiv.org/content/early/2016/06/20/060012.