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


BACKGROUND
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.
National Center for Integrative Biomedical Informatics, University of Michigan, Ann Arbor, MI 48109, USA. jinggao@umich.edu
Jing
J
Gao
V Glenn
VG
Tarcea
Alla
A
Karnovsky
Barbara R
BR
Mirel
Terry E
TE
Weymouth
Christopher W
CW
Beecher
James D
JD
Cavalcoli
Brian D
BD
Athey
Gilbert S
GS
Omenn
Charles F
CF
Burant
H V
HV
Jagadish
D016208:Databases, Factual; D006801:Humans; D053858:Metabolic Networks and Pathways; D055432:Metabolomics / Q000379:methods*; D012984:Software