Fig. 2.

Distribution of P-values under three null distribution scenarios for the hypergeometric and SPIA models. N_de=300 gene IDs were selected at random out of 20 000 possible IDs containing all genes on all 52 pathways analyzed. The randomly selected gene IDs were assigned log fold-changes from (i) a random normal distribution N(0,1); (ii) a bimodal distribution obtained by sampling from the tails of a N(0,1) distribution; and (iii) random normal N(3,0.5). For each scenario, the experiment was repeated 200 times and P_NDE, P_PERT and P_G were computed for all pathways receiving at least one DE gene. The resulting P-values for all pathways and all iterations were pooled together and shown as histograms for ORA (P_NDE) and SPIA (P_G) on rows 2 and 3, respectively. The false positives rates for SPIA at α = 5% were 4.7%, 5.0% and 4.6%, in scenarios I, II and III, respectively. For ORA, the same positive rates were 4.5% in all three scenarios. False positive rates as an average over these three scenarios are provided in Table 1 for several values of N_de.