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

A. C. Zambon, S. Gaj, I. Ho, K. Hanspers, K. Vranizan, C.T.A. Evelo, B.R. Conklin, A.R. Pico, N. Salomonis

Research output: Contribution to journalArticleAcademicpeer-review

69 Citations (Scopus)

Abstract

SUMMARY: 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 (ORA) 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. 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 CONTACT: nsalomonis@gladstone.ucsf.edu.
Original languageEnglish
Pages (from-to)2209-2210
Number of pages2
JournalBioinformatics
Volume28
Issue number16
DOIs
Publication statusPublished - 15 Aug 2012

Keywords

  • MICROARRAY DATA
  • GENE-ONTOLOGY
  • PROFILE

Cite this

Zambon, A. C., Gaj, S., Ho, I., Hanspers, K., Vranizan, K., Evelo, C. T. A., Conklin, B. R., Pico, A. R., & Salomonis, N. (2012). GO-Elite: a flexible solution for pathway and ontology over-representation. Bioinformatics, 28(16), 2209-2210. https://doi.org/10.1093/bioinformatics/bts366