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. 2012 Aug 15;28(16):2209-10.
doi: 10.1093/bioinformatics/bts366. Epub 2012 Jun 27.

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

Alexander C Zambon  1 , Stan Gaj, Isaac Ho, Kristina Hanspers, Karen Vranizan, Chris T Evelo, Bruce R Conklin, Alexander R Pico, Nathan Salomonis
Affiliations

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

Alexander C Zambon et al. Bioinformatics. .

Abstract

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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Figures

Fig. 1
Fig. 1
GO-Elite workflow and information sources. Before performing ORA, users create two text files containing a list of input IDs (e.g. regulated genes) and a denominator list (e.g. all genes examined), source ID type (e.g. Affymetrix) and numerical values (optional). These IDs are mapped to a primary ID system (EntrezGene, Ensembl, HMD or custom) for ORA upon pathways, ontologies or loaded gene sets. Regulated genes and metabolites can be immediately viewed on WikiPathways using the stand-alone or GenMAPP-CS interface. Pathway or ontology summarized expression values can be clustered and visualized outside of GO-Elite
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