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MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks

High-throughput metabolomic experiments aim at identifying and ultimately quantifying all metabolites present in biological systems. The metabolites are interconnected through metabolic reactions, generally grouped into metabolic pathways. Classical metabolic maps provide a relational context to hel...

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Autores principales: Cottret, Ludovic, Wildridge, David, Vinson, Florence, Barrett, Michael P., Charles, Hubert, Sagot, Marie-France, Jourdan, Fabien
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896158/
https://www.ncbi.nlm.nih.gov/pubmed/20444866
http://dx.doi.org/10.1093/nar/gkq312
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author Cottret, Ludovic
Wildridge, David
Vinson, Florence
Barrett, Michael P.
Charles, Hubert
Sagot, Marie-France
Jourdan, Fabien
author_facet Cottret, Ludovic
Wildridge, David
Vinson, Florence
Barrett, Michael P.
Charles, Hubert
Sagot, Marie-France
Jourdan, Fabien
author_sort Cottret, Ludovic
collection PubMed
description High-throughput metabolomic experiments aim at identifying and ultimately quantifying all metabolites present in biological systems. The metabolites are interconnected through metabolic reactions, generally grouped into metabolic pathways. Classical metabolic maps provide a relational context to help interpret metabolomics experiments and a wide range of tools have been developed to help place metabolites within metabolic pathways. However, the representation of metabolites within separate disconnected pathways overlooks most of the connectivity of the metabolome. By definition, reference pathways cannot integrate novel pathways nor show relationships between metabolites that may be linked by common neighbours without being considered as joint members of a classical biochemical pathway. MetExplore is a web server that offers the possibility to link metabolites identified in untargeted metabolomics experiments within the context of genome-scale reconstructed metabolic networks. The analysis pipeline comprises mapping metabolomics data onto the specific metabolic network of an organism, then applying graph-based methods and advanced visualization tools to enhance data analysis. The MetExplore web server is freely accessible at http://metexplore.toulouse.inra.fr.
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spelling pubmed-28961582010-07-02 MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks Cottret, Ludovic Wildridge, David Vinson, Florence Barrett, Michael P. Charles, Hubert Sagot, Marie-France Jourdan, Fabien Nucleic Acids Res Articles High-throughput metabolomic experiments aim at identifying and ultimately quantifying all metabolites present in biological systems. The metabolites are interconnected through metabolic reactions, generally grouped into metabolic pathways. Classical metabolic maps provide a relational context to help interpret metabolomics experiments and a wide range of tools have been developed to help place metabolites within metabolic pathways. However, the representation of metabolites within separate disconnected pathways overlooks most of the connectivity of the metabolome. By definition, reference pathways cannot integrate novel pathways nor show relationships between metabolites that may be linked by common neighbours without being considered as joint members of a classical biochemical pathway. MetExplore is a web server that offers the possibility to link metabolites identified in untargeted metabolomics experiments within the context of genome-scale reconstructed metabolic networks. The analysis pipeline comprises mapping metabolomics data onto the specific metabolic network of an organism, then applying graph-based methods and advanced visualization tools to enhance data analysis. The MetExplore web server is freely accessible at http://metexplore.toulouse.inra.fr. Oxford University Press 2010-07-01 2010-05-05 /pmc/articles/PMC2896158/ /pubmed/20444866 http://dx.doi.org/10.1093/nar/gkq312 Text en © The Author(s) 2010. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/2.5 This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Articles
Cottret, Ludovic
Wildridge, David
Vinson, Florence
Barrett, Michael P.
Charles, Hubert
Sagot, Marie-France
Jourdan, Fabien
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks
title MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks
title_full MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks
title_fullStr MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks
title_full_unstemmed MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks
title_short MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks
title_sort metexplore: a web server to link metabolomic experiments and genome-scale metabolic networks
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2896158/
https://www.ncbi.nlm.nih.gov/pubmed/20444866
http://dx.doi.org/10.1093/nar/gkq312
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