Gene set enrichment analysis


A common approach to functional genomics data is gene enrichment analysis based on the functional annotation of the differentially expressed genes. This is useful for example to find out if the most differentially expressed genes are all associated with a certain signalling pathway or molecular function. The Gene Ontology, containing standardised annotation of gene products, is commonly used for this purpose.

Popular tools are:

  • DAVID (free online tool) (23)
  • Gene Set Enrichment Analysis (GSEA) (free) (24)
  • Ingenuity (licence required) (25)