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

• Published in: Bioinformatics Vol. 25; no. 8; pp. 1091 - 1093
• Main Authors: Bindea, Gabriela, Mlecnik, Bernhard, Hackl, Hubert, Charoentong, Pornpimol, Tosolini, Marie, Kirilovsky, Amos, Fridman, Wolf-Herman, Pagès, Franck, Trajanoski, Zlatko, Galon, Jérôme
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15-04-2009; Oxford Publishing Limited (England)
• Subjects: Applications Note; Biological and medical sciences; Computational Biology - methods; Databases, Genetic; Fundamental and applied biological sciences. Psychology; Gene Regulatory Networks; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Models, Biological; Multigene Family; Software; Gene; Annotation; Network
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btp101

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.