GO-Elite: a flexible solution for pathway and ontology over-representation

Alexander C. Zambon, Stan Gaj, Isaac Ho, Kristina Hanspers, Karen Vranizan, Chris T. Evelo, Bruce R. Conklin, Alexander R. Pico, Nathan Salomonis
2012 Computer applications in the biosciences : CABIOS  
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 can
more » ... visualized on WikiPathways or as networks. Built-in support is provided for over 60 species and 50 ID systems, covering gene, disease and phenotype ontologies, multiple pathway databases, biomarkers, and transcription factor and microRNA targets. GO-Elite is available as a web interface, GenMAPP-CS plugin and as a cross-platform application.
doi:10.1093/bioinformatics/bts366 pmid:22743224 pmcid:PMC3413395 fatcat:dayn6pkilrb4pctr77bo457g5e