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Bioinformatics Advance Access originally published online on February 23, 2009
Bioinformatics 2009 25(8):1091-1093; doi:10.1093/bioinformatics/btp101
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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

Gabriela Bindea 1–4,{dagger}, Bernhard Mlecnik 1–3,{dagger}, Hubert Hackl 4, Pornpimol Charoentong 4, Marie Tosolini 1–3, Amos Kirilovsky 1–3, Wolf-Herman Fridman 1–3,5, Franck Pagès 1–3,5, Zlatko Trajanoski 4 and Jérôme Galon 1–3,5,*

1INSERM, AVENIR Team, Integrative Cancer Immunology, U872, 75006 Paris, 2Université Paris Descartes, 3Université Pierre et Marie Curie Paris 6, Cordeliers Research Center, Paris, France, 4Institute for Genomics and Bioinformatics, Graz University of Technology, Graz, Austria and 5Assistance Publique-Hôpitaux de Paris, HEGP, Paris, France

*To whom correspondence should be addressed.


  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: jerome.galon{at}crc.jussieu.fr

Supplementary information: Supplementary data are available at Bioinformatics online.

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as Joint First Authors.

Associate Editor: Trey Ideker

Received on November 13, 2008; revised on February 8, 2009; accepted on February 16, 2009

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