Biological pathways analysis was undertaken for all variables using ALIGATOR (Holmans et al., 2009) and for the speed factor only using the SNPratio test (O’Dushlaine et al., 2009). Because ALIGATOR can use meta-analysis p-values to generate results, all variables were run through this program. SNPratio, on the other hand, is computer intensive requiring raw genotype data, therefore, only one variable was analysed (the composite speed factor) and this was done separately by cohort. In brief, ALIGATOR counts the number of significant genes (based on a nominal SNP association) in Gene Ontology (GO) categories that arise more often than would be expected by chance (empirical p-values of GO category membership are established via permutation of randomly drawn genes). We used a p-value of .01 for inclusion of nominally significant SNPs, 5000 replicate gene lists and 1000 replicate studies (used to judge study-wide significance levels for individual categories). The SNPratio test compares the proportion of nominally significant (p < .05) SNPs within genes to all SNPs within genes that relate to a specific biological pathway (from 220 experimentally validated pathways described in
