MetScape Plugin for Cytoscape

MetScape is a Cytoscape plugin used to visualize and analyze metabolomic data. It uses the data from Edinburgh Human Metabolic Network reconstruction (Ma et al., Mol Syst Biol. 2007; 3: 135). MetScape allows you to visualize compound networks and display related information about reactions, enzymes, and pathways.

Using a modified DynamicXpr plugin, you can upload experimental metabolomic data and visualize the networks evolution over time or conditions by observing the changing node colors or sizes. MetScape allows you to display the entire metabolic network or pathways-specific networks. You can apply a pathway filter to a network to create sub networks from resulting subsets of compounds. In the future, we will integrate MiMI, a database of gene, gene product, interaction and pathways, to show gene related information.

Current Version

1.0

Intended Audience

Analysts, Biomedical researchers

References

Bioinformatics Framework for the Analysis and Interpretation of Metabolomic Data
Alla Karnovsky, Jing Gao, Glenn Tarcea, Christopher Beecher, Charles Burant, Barbara Mirel, H.V. Jagadish, Gilbert S. Omenn - Download Poster