ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

TLDR

ClueGO integrates Gene Ontology terms and KEGG/BioCarta pathways to build a functionally organized GO/pathway network, enabling analysis of one or two gene lists with automatic updates and optional visualization via the GOlorize plug‑in. ClueGO is an easy‑to‑use Cytoscape plug‑in that markedly enhances biological interpretation of large gene lists. ClueGO is downloadable from http://www.ici.upmc.fr/cluego/cluegoDownload.shtml, contact Jerome Galon at [e-mail], and supplementary data are available online.

Abstract

Abstract Summary: We have developed ClueGO, an easy to use Cytoscape plug-in that strongly improves biological interpretation of large lists of genes. ClueGO integrates Gene Ontology (GO) terms as well as KEGG/BioCarta pathways and creates a functionally organized GO/pathway term network. It can analyze one or compare two lists of genes and comprehensively visualizes functionally grouped terms. A one-click update option allows ClueGO to automatically download the most recent GO/KEGG release at any time. ClueGO provides an intuitive representation of the analysis results and can be optionally used in conjunction with the GOlorize plug-in. Availability: http://www.ici.upmc.fr/cluego/cluegoDownload.shtml Contact: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.