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

TitleMetscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks.
Publication TypeJournal Article
Year of Publication2010
AuthorsGao, Jing, V Tarcea Glenn, Karnovsky Alla, Mirel Barbara R., Weymouth Terry E., Beecher Christopher W., Cavalcoli James D., Athey Brian D., Omenn Gilbert S., Burant Charles F., and Jagadish H V.
JournalBioinformatics
Volume26
Issue7
Pagination971-3
Date Published2010 Apr 1
ISSN1367-4811
KeywordsDatabases, Factual, Humans, Metabolic Networks and Pathways, Metabolomics, Software
Abstract

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.

DOI10.1093/bioinformatics/btq048
Alternate JournalBioinformatics
PubMed ID20139469
PubMed Central IDPMC2844990
Grant ListP30 DK089503 / DK / NIDDK NIH HHS / United States
R01DK079084 / DK / NIDDK NIH HHS / United States
U54 DA021519 / DA / NIDA NIH HHS / United States