Axe 3: Intégration et Représentation des Connaissances MetExplore: Collaborative platform for building, analyzing, simulating and improving metabolic networks
http://metexplore.toulouse.inra.fr
Project Coordination : Fabien Jourdan1, Jean-Charles Portais2,3,4
Executive coordination : Ludovic Cottret5
Development and maintenance : Ludovic Cottret5, Florence Vinson1
1 : INRA, UMR1331, Toxalim, F-31000 Toulouse, France
2 : Université de Toulouse; INSA,UPS,INP; LISBP, 135 Avenue de Rangueil, F-31077 Toulouse, France
3 : INRA, UMR792, Ingénierie des Systèmes Biologiques et des Procédés, F-31400 Toulouse, France
4 : CNRS, UMR5504, F-31400 Toulouse, France
5 : Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR INRA-CNRS 441/2594, F-31320 Castanet Tolosan, France
The availability of complete genome sequences for several organisms offers an invaluable resource for the reconstruction of biochemical networks in organisms at the genome scale level. These genome-scale networks are essential for high-throughput “omics” data interpretation, and they can be converted into metabolic models for simulating the operation of cellular metabolism in response to different stimuli.
MetExplore allows the import, annotation and modification of metabolic networks by several users in a collaborative way. The metabolic networks used to establish models can be duplicated from the MetExplore database or imported from external SBML files.
Several computational analyses can be performed on the public or private MetExplore networks. First, mapping functions allow to highlight metabolites (by their mass or their identifier) or reactions (by the associated gene names) onto a global view of the metabolic network. Secondly, MetExplore offers graph-based functions including choke point analysis, computation of biosynthetic capacity and potential precursor identification for any set of selected metabolites. At last, flux balance analysis (FBA) functions were introduced in MetExplore to simulate flux distributions in metabolic networks under different environmental/genetic conditions. Strength of MetExplore is to provide a user-friendly tabular view that helps to fill in the FBA parameters by making easier the selection of reactions by their names, the metabolites, the genes or, the metabolic pathways. The FBA-based functions provided in MetExplore include i) computing of optimal functions, ii) knock out analysis, iii) robustness analysis, iv) identification of essential and live reactions, and v) flux variability analysis (FVA).
MetExplore has been running since June 2009, it has been visited 3404 times by 1406 distinct visitors and has been intensively tested and used by three INRA units in Toulouse and Lyon, and by members of four international laboratories: Lyon University (France), Glasgow University (United Kingdom), LNCC (Brazil), ETH (Switzerland).Reference:
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Cottret L, Wildridge D, Vinson F, Barrett MP, Charles H, Sagot MF, Jourdan F. Nucleic Acids Res. 2010
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