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

Alexander C. Zambon(University of California, San Francisco), Stan Gaj(University of California, San Francisco), Isaac Ho(University of California, San Francisco), Kristina Hanspers(University of California, San Francisco), Karen Vranizan(University of California, San Francisco), Chris T. Evelo(University of California, San Francisco), Bruce R. Conklin(University of California, San Francisco), Alexander R. Pico(University of California, San Francisco), Nathan Salomonis(University of California, San Francisco)
Bioinformatics
June 27, 2012
10.1093/bioinformatics/bts366
Cited by 283Open Access
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Abstract

UNLABELLED: 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 non-overlapping terms. The results can be 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. AVAILABILITY: http://www.genmapp.org/go_elite

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