We test the query list plus the related genes found by GeneMANIA for enrichment of a selection of Gene Ontology term annotations against the background of all genes in the organisms with any Gene Ontology annotation. We use a Benjamini–Hochberg FDR multiple testing correction and report the FDR (also known as the ‘q-value’) associated with each term. We only report GO terms with FDR < 0.05. When doing the enrichment analysis, we only consider GO terms with at least 10 annotations in the organism and no more than 300 to control the size of the multiple testing correction. We currently do not filter the GO terms for redundancy nor do we attempt to merge them into clusters [c.f. (11–13)]. To improve ease of use, we plan to reduce redundancy in this list in the future.
