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Metabolic network visualization eliminating node redundance and preserving metabolic pathways

dc.contributor.authorBOURQUI, Romain
hal.structure.identifierBaobab [LBBE]
dc.contributor.authorCOTTRET, L.
hal.structure.identifierBaobab [LBBE]
dc.contributor.authorLACROIX, Vincent
dc.contributor.authorAUBER, D.
dc.contributor.authorMARY, P.
hal.structure.identifierBaobab [LBBE]
dc.contributor.authorSAGOT, M.-F.
hal.structure.identifierLaboratoire de Biométrie et Biologie Evolutive - UMR 5558 [LBBE]
dc.contributor.authorJOURDAN, F.
dc.date.accessioned2024-04-15T09:55:41Z
dc.date.available2024-04-15T09:55:41Z
dc.date.issued2007
dc.identifier.issn1741-7007
dc.identifier.urihttps://oskar-bordeaux.fr/handle/20.500.12278/198776
dc.description.abstractEnBackground: The tools that are available to draw and to manipulate the representations of metabolism are usually restricted to metabolic pathways. This limitation becomes problematic when studying processes that span several pathways. The various attempts that have been made to draw genome-scale metabolic networks are confronted with two shortcomings: 1- they do not use contextual information which leads to dense, hard to interpret drawings, 2- they impose to fit to very constrained standards, which implies, in particular, duplicating nodes making topological analysis considerably more difficult. Results: We propose a method, called MetaViz, which enables to draw a genome-scale metabolic network and that also takes into account its structuration into pathways. This method consists in two steps: a clustering step which addresses the pathway overlapping problem and a drawing step which consists in drawing the clustered graph and each cluster. Conclusion: The method we propose is original and addresses new drawing issues arising from the no-duplication constraint. We do not propose a single drawing but rather several alternative ways of presenting metabolism depending on the pathway on which one wishes to focus. We believe that this provides a valuable tool to explore the pathway structure of metabolism.
dc.language.isoen
dc.publisherBioMed Central
dc.subject1-1-1 Article périodique à comité de lecture
dc.title.enMetabolic network visualization eliminating node redundance and preserving metabolic pathways
dc.typeArticle de revue
dc.identifier.doi10.1186/1752-0509-1-29
dc.subject.halSciences du Vivant [q-bio]/Autre [q-bio.OT]
bordeaux.journalBMC Biology
bordeaux.page1-19
bordeaux.volume1 - n°29
bordeaux.hal.laboratoriesLaboratoire Bordelais de Recherche en Informatique (LaBRI) - UMR 5800*
bordeaux.institutionUniversité de Bordeaux
bordeaux.institutionBordeaux INP
bordeaux.institutionCNRS
bordeaux.peerReviewedoui
hal.identifierhal-00434765
hal.version1
hal.popularnon
hal.audienceNon spécifiée
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-00434765v1
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