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We introduce GO-Elite, a flexible and powerful pathway analysis tool for a wide array of species, identifiers (IDs), pathways, ontologies and gene sets. In addition to the Gene Ontology (GO), GO-Elite allows the user to perform over-representation analysis on any structured ontology annotations, pathway database or biological IDs (e.g. gene, protein or metabolite). GO-Elite exploits the structured nature of biological ontologies to report a minimal set of nonoverlapping terms. The results candoi:10.1093/bioinformatics/bts366 pmid:22743224 pmcid:PMC3413395 fatcat:dayn6pkilrb4pctr77bo457g5e