The idea of pathway enrichment analysis is to test whether a specified set of biologically related genes (pathway) shows greater than expected association with disease compared to a random set of genes. ALIGATOR (Holmans et al. 2009) was used to perform such an analysis using a combined set of GO categories and KEGG pathways. ALIGATOR converts a list of significant SNPs into a list of significant genes (defined as those genes containing one or more significant SNPs) and tests this list for enrichment of gene sets defined by the categories/pathways. Enrichment is defined as a gene set containing a larger number of significant genes than expected by chance. Replicate gene lists of the same length as the original are generated by randomly sampling SNPs (thus correcting for variable gene size). The lists are used to obtain p-values for enrichment for each gene set (by comparing the number of significant genes observed on the actual gene list to that observed on each replicate list), to correct these for testing multiple non-independent categories, and to test whether the number of significantly enriched
