Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data.

TitleMetscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data.
Publication TypeJournal Article
Year of Publication2012
AuthorsKarnovsky, Alla, Weymouth Terry, Hull Tim, V Tarcea Glenn, Scardoni Giovanni, Laudanna Carlo, Sartor Maureen A., Stringer Kathleen A., Jagadish H V., Burant Charles, Athey Brian, and Omenn Gilbert S.
Date Published2012 Feb 1
KeywordsAdenocarcinoma, Animals, Gene Expression Profiling, Humans, Inflammation, Metabolic Networks and Pathways, Metabolomics, Mice, Pancreatic Neoplasms, Proteomics, Sepsis, Software

MOTIVATION: Metabolomics is a rapidly evolving field that holds promise to provide insights into genotype-phenotype relationships in cancers, diabetes and other complex diseases. One of the major informatics challenges is providing tools that link metabolite data with other types of high-throughput molecular data (e.g. transcriptomics, proteomics), and incorporate prior knowledge of pathways and molecular interactions.RESULTS: We describe a new, substantially redesigned version of our tool Metscape that allows users to enter experimental data for metabolites, genes and pathways and display them in the context of relevant metabolic networks. Metscape 2 uses an internal relational database that integrates data from KEGG and EHMN databases. The new version of the tool allows users to identify enriched pathways from expression profiling data, build and analyze the networks of genes and metabolites, and visualize changes in the gene/metabolite data. We demonstrate the applications of Metscape to annotate molecular pathways for human and mouse metabolites implicated in the pathogenesis of sepsis-induced acute lung injury, for the analysis of gene expression and metabolite data from pancreatic ductal adenocarcinoma, and for identification of the candidate metabolites involved in cancer and inflammation.AVAILABILITY: Metscape is part of the National Institutes of Health-supported National Center for Integrative Biomedical Informatics (NCIBI) suite of tools, freely available at It can be downloaded from or installed via Cytoscape plugin manager.CONTACT:; akarnovs@umich.eduSUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Alternate JournalBioinformatics
PubMed ID22135418
PubMed Central IDPMC3268237
Grant List5P30DK089503 / DK / NIDDK NIH HHS / United States
5R01DK079084 / DK / NIDDK NIH HHS / United States
NIHP30ES017885 / ES / NIEHS NIH HHS / United States
P30 ES017885 / ES / NIEHS NIH HHS / United States
R01 DK077200 / DK / NIDDK NIH HHS / United States
U54DA21519 / DA / NIDA NIH HHS / United States