The SNP ratio test: pathway analysis of genome-wide association datasets

Abstract Summary: We present a tool that assesses the enrichment of significant associations from genome-wide association studies (GWAS) in a pathway context. The SNP ratio test (SRT) compares the proportion of significant to all SNPs within genes that are part of a pathway and computes an empirical P-value based on comparisons to ratios in datasets where the assignment of case/control status has been randomized. We applied the SRT to a Parkinson's disease GWAS dataset, using the KEGG database, revealing significance for Parkinson's disease and related pathways. Availability: https://sourceforge.net/projects/snpratiotest/ Contact: codushlaine@gmail.com; colm.odushlaine@tcd.ie Supplementary information: Supplementary data are available at Bioinformatics online.