Significantly more GO pathways are identified than expected.

The analysis used only autosomes and was restricted to GO categories with at least two hits. SNPs that mapped to within 20kb of a gene were assigned to that gene: if SNPs mapped within 20kb of more than one gene all such genes were included. SNPs in the APOE region (49.6–50.6 Mb on chromosome 19, 34 genes) were removed from the analysis. Only the most significant of any GO categories containing the same list of significant genes was permitted and any one SNP was not allowed to add more than one gene to any GO category. P-values were generated using 5000 permutations of the data except for * 50,000 permutations.