To test for overrepresentation of biological functions, the prioritized genes (or a list of genes of interest) are tested against gene sets obtained from MsigDB (i.e., hallmark gene sets, positional gene sets, curated gene sets, motif gene sets, computational gene sets, GO gene sets, oncogenic signatures, and immunologic signatures) and WikiPathways, using hypergeometric tests. The set of background genes (i.e., the genes against which the set of prioritized genes are tested against) is 19,283 protein-coding genes. Background genes can also be selected from gene types as described in the “Gene Mapping” section. Custom sets of background genes can also be provided by the users. Multiple testing correction (i.e., Benjamini–Hochberg by default) is performed per data source of tested gene sets (e.g., canonical pathways, GO biological processes, hallmark genes). FUMA reports gene sets with adjusted P-value ≤ 0.05 and the number of genes that overlap with the gene set > 1 by default.
