MetDisease--connecting metabolites to diseases via literature.

TitleMetDisease--connecting metabolites to diseases via literature.
Publication TypeJournal Article
Year of Publication2014
AuthorsDuren, William, Weymouth Terry, Hull Tim, Omenn Gilbert S., Athey Brian, Burant Charles, and Karnovsky Alla
JournalBioinformatics
Volume30
Issue15
Pagination2239-41
Date Published2014 Aug 1
ISSN1367-4811
KeywordsDatabases, Chemical, Disease, Genome, Human, Humans, Medical Subject Headings, Metabolic Networks and Pathways, Metabolomics, Software
Abstract

MOTIVATION: In recent years, metabolomics has emerged as an approach to perform large-scale characterization of small molecules in biological systems. Metabolomics posed a number of bioinformatics challenges associated in data analysis and interpretation. Genome-based metabolic reconstructions have established a powerful framework for connecting metabolites to genes through metabolic reactions and enzymes that catalyze them. Pathway databases and bioinformatics tools that use this framework have proven to be useful for annotating experimental metabolomics data. This framework can be used to infer connections between metabolites and diseases through annotated disease genes. However, only about half of experimentally detected metabolites can be mapped to canonical metabolic pathways. We present a new Cytoscape 3 plug-in, MetDisease, which uses an alternative approach to link metabolites to disease information. MetDisease uses Medical Subject Headings (MeSH) disease terms mapped to PubChem compounds through literature to annotate compound networks.AVAILABILITY AND IMPLEMENTATION: MetDisease can be downloaded from http://apps.cytoscape.org/apps/metdisease or installed via the Cytoscape app manager. Further information about MetDisease can be found at http://metdisease.ncibi.orgCONTACT: akarnovs@med.umich.eduSUPPLEMENTARY INFORMATION: Supplementary Data are available at Bioinformatics online.

DOI10.1093/bioinformatics/btu179
Alternate JournalBioinformatics
PubMed ID24713438
PubMed Central IDPMC4103594
Grant ListDK097153 / DK / NIDDK NIH HHS / United States
P30 DK020572 / DK / NIDDK NIH HHS / United States
P30 DK089503 / DK / NIDDK NIH HHS / United States
P30 ES017885 / ES / NIEHS NIH HHS / United States
P30 ES017885 / ES / NIEHS NIH HHS / United States
U54 DA02151901A1 / DA / NIDA NIH HHS / United States