A commonly used statistic to derive pathway scores from a ranked list of genes (or SNPs) is to first apply a fixed threshold in order to define a subset of elements that is considered to be significantly associated with the given trait. The pathway statistic is then computed using a hypergeometric test evaluating whether the pathway contains more significant elements than expected. This approach is implemented, for example, in the tool MAGENTA[3]. Another common strategy is to use the rank-sum (Wilcoxon) test[3,28,29].
