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Bioinformatics Advance Access originally published online on August 3, 2009
Bioinformatics 2009 25(19):2617-2618; doi:10.1093/bioinformatics/btp464
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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.

Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks

Mathieu Clément-Ziza 1,2,{dagger},*, Christophe Malabat 3,{dagger}, Christian Weber 4, Ivan Moszer 5, Tero Aittokallio 6, Catherine Letondal 7 and Sandrine Rousseau 5,*

1Biotechnology Center, TU Dresden, Dresden, Germany, 2INSERM U-781, Université René-Descartes, Hôpital Necker-Enfants Malades, 3Institut Pasteur, Unité de Génétique des Interactions Macromoléculaires, CNRS, URA2171, 4Institut Pasteur, INSERM U786, Biologie Cellulaire du Parasitisme, 5Institut Pasteur, Plate-Forme Intégration et Analyse Génomiques, 6Institut Pasteur, Unité de Biologie Systémique and 7Institut Pasteur, Pôle Informatique, Paris, France

*To whom correspondence should be addressed.


  Abstract

Summary: Genoscape is an open-source Cytoscape plug-in that visually integrates gene expression data sets from GenoScript, a transcriptomic database, and KEGG pathways into Cytoscape networks. The generated visualisation highlights gene expression changes and their statistical significance. The plug-in also allows one to browse GenoScript or import transcriptomic data from other sources through tab-separated text files. Genoscape has been successfully used by researchers to investigate the results of gene expression profiling experiments.

Availability: Genoscape is an open-source software freely available from the Genoscape webpage (http://www.pasteur.fr/recherche/unites/Gim/genoscape/). Installation instructions and tutorial can also be found at this URL.

Contact: Mathieu.clement-ziza{at}biotec.tu-dresden.de; sandrine.rousseau{at}pasteur.fr

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Trey Ideker

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

Received on February 9, 2009; revised on July 1, 2009; accepted on July 24, 2009

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