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

Jing Gao | Zendy; V. Glenn Tarcea | Zendy; Alla Karnovsky | Zendy; Barbara R. Mirel | Zendy; Terry E. Weymouth | Zendy; Chris Beecher | Zendy; James D. Cavalcoli | Zendy; Brian D. Athey | Zendy; Gilbert S. Omenn | Zendy; Charles Burant | Zendy; H. V. Jagadish | Zendy

Open Access

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

Author(s) -

Jing Gao,

V. Glenn Tarcea,

Alla Karnovsky,

Barbara R. Mirel,

Terry E. Weymouth,

Chris Beecher,

James D. Cavalcoli,

Brian D. Athey,

Gilbert S. Omenn,

Charles Burant,

H. V. Jagadish

Publication year - 2010

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btq048

Subject(s) - upload , computer science , context (archaeology) , metabolic network , plug in , visualization , metabolomics , data mining , computational biology , information retrieval , database , bioinformatics , world wide web , biology , paleontology , programming language

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.

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