GSEA-SNP: applying gene set enrichment analysis to SNP data from genome-wide association studies.
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.
Holden
Marit
M
Norwegian Computing Center, Oslo, Norway, Department of Pharmacology, University of Mainz, Mainz, Germany.
Deng
Shiwei
S
Wojnowski
Leszek
L
Kulle
Bettina
B
D016678:Genome; D055106:Genome-Wide Association Study / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012984:Software