Number of significant gene sets at different p-value thresholds.

The FWER column corresponds to p-values below 0.05 after family-wise error correction, using Bonferroni correction for MAGMA, PLINK and MAGENTA and built-in FWER methods for INRICH and ALIGATOR. The ‘Tested gene sets’ column shows the number of gene sets for which p-values were computed, which were lower for INRICH, ALIGATOR and MAGENTA because some gene sets contained insufficiently many SNPs/intervals/genes with p-value below the chosen cut-off. Note that such gene sets do remain part of the analysis and count towards the total number of tests conducted, their p-values are effectively set to 1.a in this analysis the default correction for gene size and gene density was turned offNumber of significant gene sets at different p-value thresholds.