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

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...

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Autores principales: Clément-Ziza, Mathieu, Malabat, Christophe, Weber, Christian, Moszer, Ivan, Aittokallio, Tero, Letondal, Catherine, Rousseau, Sandrine
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2009
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752617/
https://www.ncbi.nlm.nih.gov/pubmed/19654116
http://dx.doi.org/10.1093/bioinformatics/btp464
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author Clément-Ziza, Mathieu
Malabat, Christophe
Weber, Christian
Moszer, Ivan
Aittokallio, Tero
Letondal, Catherine
Rousseau, Sandrine
author_facet Clément-Ziza, Mathieu
Malabat, Christophe
Weber, Christian
Moszer, Ivan
Aittokallio, Tero
Letondal, Catherine
Rousseau, Sandrine
author_sort Clément-Ziza, Mathieu
collection PubMed
description 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@biotec.tu-dresden.de; sandrine.rousseau@pasteur.fr Supplementary information: Supplementary data are available at Bioinformatics online.
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spelling pubmed-27526172009-10-01 Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks Clément-Ziza, Mathieu Malabat, Christophe Weber, Christian Moszer, Ivan Aittokallio, Tero Letondal, Catherine Rousseau, Sandrine Bioinformatics Applications Note 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@biotec.tu-dresden.de; sandrine.rousseau@pasteur.fr Supplementary information: Supplementary data are available at Bioinformatics online. Oxford University Press 2009-10-01 2009-08-03 /pmc/articles/PMC2752617/ /pubmed/19654116 http://dx.doi.org/10.1093/bioinformatics/btp464 Text en 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
Clément-Ziza, Mathieu
Malabat, Christophe
Weber, Christian
Moszer, Ivan
Aittokallio, Tero
Letondal, Catherine
Rousseau, Sandrine
Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks
title Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks
title_full Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks
title_fullStr Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks
title_full_unstemmed Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks
title_short Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks
title_sort genoscape: a cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752617/
https://www.ncbi.nlm.nih.gov/pubmed/19654116
http://dx.doi.org/10.1093/bioinformatics/btp464
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