Journal Article

Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks

Jing Gao, V. Glenn Tarcea, Alla Karnovsky, Barbara R. Mirel, Terry E. Weymouth, Christopher W. Beecher, James D. Cavalcoli, Brian D. Athey, Gilbert S. Omenn, Charles F. Burant and H. V. Jagadish

in Bioinformatics

Volume 26, issue 7, pages 971-973
Published in print April 2010 | ISSN: 1367-4803
Published online February 2010 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btq048
Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks

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Summary: Metscape is a plug-in for Cytoscape, used to visualize and interpret metabolomic data in the context of human metabolic networks. We have developed a metabolite database by extracting and integrating information from several public sources. By querying this database, Metscape allows users to trace the connections between metabolites and genes, visualize compound networks and display compound structures as well as information for reactions, enzymes, genes and pathways. Applying the pathway filter, users can create subnetworks that consist of compounds and reactions from a given pathway. Metscape allows users to upload experimental data, and visualize and explore compound networks over time, or experimental conditions. Color and size of the nodes are used to visualize these dynamic changes. Metscape can display the entire metabolic network or any of the pathway-specific networks that exist in the database.

Availability: Metscape can be installed from within Cytoscape 2.6.x under ‘Network and Attribute I/O’ category. For more information, please visit http://metscape.ncibi.org/tryplugin.html

Contact: jinggao@umich.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Journal Article.  1514 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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