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Bioinformatics Advance Access published online on February 23, 2009
Bioinformatics, 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 1,2,3,4,6, Bernhard Mlecnik 1,2,3,6, Hubert Hackl 4, Pornpimol Charoentong 4, Marie Tosolini 1,2,3, Amos Kirilovsky 1,2,3, Wolf-Herman Fridman 1,2,3,5, Franck Pagès 1,2,3,5, Zlatko Trajanoski 4 and Jérôme Galon 1,2,3,5,*

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

*To whom correspondence should be addressed. Dr. Jerome Galon, E-mail: jerome.galon{at}crc.jussieu.f


  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: http://www.ici.upmc.fr/cluego/ClueGODocumentation.pdf

Associate Editor: Dr. Trey Ideker

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

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