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

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...

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Autores principales: Bindea, Gabriela, Mlecnik, Bernhard, Hackl, Hubert, Charoentong, Pornpimol, Tosolini, Marie, Kirilovsky, Amos, Fridman, Wolf-Herman, Pagès, Franck, Trajanoski, Zlatko, Galon, Jérôme
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666812/
https://www.ncbi.nlm.nih.gov/pubmed/19237447
http://dx.doi.org/10.1093/bioinformatics/btp101
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author Bindea, Gabriela
Mlecnik, Bernhard
Hackl, Hubert
Charoentong, Pornpimol
Tosolini, Marie
Kirilovsky, Amos
Fridman, Wolf-Herman
Pagès, Franck
Trajanoski, Zlatko
Galon, Jérôme
author_facet Bindea, Gabriela
Mlecnik, Bernhard
Hackl, Hubert
Charoentong, Pornpimol
Tosolini, Marie
Kirilovsky, Amos
Fridman, Wolf-Herman
Pagès, Franck
Trajanoski, Zlatko
Galon, Jérôme
author_sort Bindea, Gabriela
collection PubMed
description 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@crc.jussieu.fr Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-26668122009-04-29 ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks Bindea, Gabriela Mlecnik, Bernhard Hackl, Hubert Charoentong, Pornpimol Tosolini, Marie Kirilovsky, Amos Fridman, Wolf-Herman Pagès, Franck Trajanoski, Zlatko Galon, Jérôme Bioinformatics Applications Note 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@crc.jussieu.fr Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2009-04-15 2009-02-23 /pmc/articles/PMC2666812/ /pubmed/19237447 http://dx.doi.org/10.1093/bioinformatics/btp101 Text en © 2009 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ 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.
spellingShingle Applications Note
Bindea, Gabriela
Mlecnik, Bernhard
Hackl, Hubert
Charoentong, Pornpimol
Tosolini, Marie
Kirilovsky, Amos
Fridman, Wolf-Herman
Pagès, Franck
Trajanoski, Zlatko
Galon, Jérôme
ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
title ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
title_full ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
title_fullStr ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
title_full_unstemmed ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
title_short ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
title_sort cluego: a cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2666812/
https://www.ncbi.nlm.nih.gov/pubmed/19237447
http://dx.doi.org/10.1093/bioinformatics/btp101
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