A computational solution to automatically map metabolite libraries in the context of genome scale metabolic networks

Merlet, B., Paulhe, N., Vinson, F., Frainay, C., Chazalviel, M., Poupin, N., Gloaguen, Y. , Giacomoni, F. and Jourdan, F. (2016) A computational solution to automatically map metabolite libraries in the context of genome scale metabolic networks. Frontiers in Molecular Biosciences, 3, 2. (doi: 10.3389/fmolb.2016.00002) (PMID:26909353) (PMCID:PMC4754433)

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Abstract

This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc) and flat file formats (SBML and Matlab files). We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics) and Glasgow Polyomics (GP) on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks. In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks. In order to achieve this goal, we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities.

Item Type:Articles
Status:Published
Refereed:Yes
Glasgow Author(s) Enlighten ID:Gloaguen, Mr Yoann
Authors: Merlet, B., Paulhe, N., Vinson, F., Frainay, C., Chazalviel, M., Poupin, N., Gloaguen, Y., Giacomoni, F., and Jourdan, F.
College/School:College of Medical Veterinary and Life Sciences > School of Cancer Sciences
Journal Name:Frontiers in Molecular Biosciences
Publisher:Frontiers Media
ISSN:2296-889X
ISSN (Online):2296-889X
Copyright Holders:Copyright © 2016 Merlet, Paulhe, Vinson, Frainay, Chazalviel, Poupin, Gloaguen, Giacomoni and Jourdan
First Published:First published in Frontiers in Molecular Biosciences 3: 2
Publisher Policy:Reproduced under a Creative Commons License

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Project CodeAward NoProject NamePrincipal InvestigatorFunder's NameFunder RefLead Dept
172121Funding SchemesAnna DominiczakWellcome Trust (WELLCOTR)105614/Z/14/ZInstitute of Cardiovascular & Medical Sciences