PANOGA: a web-server for identification of SNP targeted pathways from genome-wide association study data

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 Pathway and Network-Oriented GWAS Analysis 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 and (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’ on request. Contact: burcub@gatech.edu Supplementary information: Supplementary data are available at Bioinformatics online.