Both ALIGATOR and MAGENTA provide methods to correct for the multiple pathways tested. ALIGATOR applies a bootstrap approach [15] whereas MAGENTA implements both Bonferroni multiple test correction and false discovery rate method [27]. To analyze the combined evidence of the multiple studies evaluated independently (Table 3) we chose the most stringent method, the Bonferroni multiple test correction, although it is most likely too conservative for the nested organization of GO terms. The corrected p-value is 6.11E−6 for the nominal p-value = 0.05 and 8179 pathways tested. Using this significance level the terms GO:0042166 and GO:0004984 were significant for the three combined studies (weighted Z-method [43]) (Table 3). Similarly, both methods provide mechanisms to correct for linkage disequilibrium; and thus avoid the situation that a same signal, which spans across multiple genes, inflates the number of significant genes in a same pathway. Because this inflation can be a source of false positive results for terms including clusters of genes, we re-executed the ALIGATOR method collapsing all physically proximal genes in the same category into a single entity. The GO terms representing
