GOElite

Introduction

GO-Elite is a software tool designed to identify a minimal non-redundant set of Gene Ontology (GO) biological terms or pathways to describe a particular set of genes. This tool calculates over-representation statistics similar to the PC program MAPPFinder and subsequently produces filtered GO and pathway results along with corresponding gene annotations and summarized expression data. GO-Elite version 1 Beta is currently provided as source-code, a stand-alone application which is run using a Windows executable file (GO-Elite.exe), mac application or as cross-platform source code in python. GO-Elite is also available as a web service and as a Cytoscape plugin.

The GO-Elite source-code has been added to AltAnalyze to provide pathway over-representation analyses for gene expression and alternative splicing analyses.

Details

In addition to performing typical over-representation analysis (ORA) this tools allows the user to run permutation tests on these results (to assess the overall likelihood of over-representation), filter-out redundant GO-terms and pathways for publication ready tables, summarize all gene expression results at the pathway level and easily view gene annotations for each pathways. In addition, other types of Ontologies (e.g., Disease or Phenotype), pathways (e.g., KEGG, Reactome) or gene-sets (e.g., transcription targets, chromosomal bands) can be supplied as optional inputs. A tutorial for GO-Elite can be found here.

GO-Elite tutorials can be found here:

http://code.google.com/p/go-elite/wiki/Tutorials

Additional technical details can be found here:

http://www.genmapp.org/go_elite