Identification of SNP Targeted Pathways From Genome-wide Association Study (GWAS) Data

Abstract

Summary: Genome-Wide Association Studies (GWAS) have revolutionized the search for the variants underlying human complex diseases. However, in a typical GWAS, only a minority of the single nucleotide polymorphisms (SNPs) with the strongest evidence of association is explained. One possible reason of complex diseases is the alterations in the activity of several biological pathways. Here we present a web-server called PANOGA to devise functionally important pathways through the identification of SNP targeted genes within these pathways. The strength of our methodology stems from its multidimensional perspective, where we combine evidence from the following five resources: i) genetic association information obtained through GWAS, ii) SNP functional information, iii) protein-protein interaction network, iv) linkage disequilibrium (LD), v) biochemical pathways. Availability: PANOGA web-server is freely available at: http://panoga.sabanciuniv.edu/. The source code is available to academic users as is' upon request. Contact: burcub@gatech.edu Supplementary information: Supplementary information: Supplementary data are available at Bioinformatics online.