We applied the same evaluation strategy for GWAS data on Crohn’s disease. We used the currently largest GWAS for Crohn’s disease[31] to define a reference standard of associated pathways. We then applied both pathway analysis methods to results from two individual cohorts participating in the meta-analysis that contained at least 1000 cases[31–33]. We observed that the chi-squared-method performed at least as well as all other strategies in this setting (Fig 4B). Overall, we saw similar results for both max and sum gene scores (S5 Fig).
