GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies

Bioinformatics. 2008 Dec 1;24(23):2784-5. doi: 10.1093/bioinformatics/btn516. Epub 2008 Oct 14.


The power of genome-wide SNP association studies is limited, among others, by the large number of false positive test results. To provide a remedy, we combined SNP association analysis with the pathway-driven gene set enrichment analysis (GSEA), recently developed to facilitate handling of genome-wide gene expression data. The resulting GSEA-SNP method rests on the assumption that SNPs underlying a disease phenotype are enriched in genes constituting a signaling pathway or those with a common regulation. Besides improving power for association mapping, GSEA-SNP may facilitate the identification of disease-associated SNPs and pathways, as well as the understanding of the underlying biological mechanisms. GSEA-SNP may also help to identify markers with weak effects, undetectable in association studies without pathway consideration. The program is freely available and can be downloaded from our website.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Genome*
  • Genome-Wide Association Study / methods*
  • Polymorphism, Single Nucleotide / genetics*
  • Software*