Utilize este identificador para referenciar este registo: http://hdl.handle.net/1822/46349

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dc.contributor.authorDias, Oscarpor
dc.contributor.authorGomes, Daniel G.por
dc.contributor.authorVilaça, P.por
dc.contributor.authorCardoso, Joãopor
dc.contributor.authorRocha, Miguelpor
dc.contributor.authorFerreira, Eugénio C.por
dc.contributor.authorRocha, Isabelpor
dc.date.accessioned2017-08-05T15:22:40Z-
dc.date.available2017-08-05T15:22:40Z-
dc.date.issued2017-
dc.identifier.citationDias, Oscar; Gomes, Daniel G.; Vilaça, P.; Cardoso, João; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, Isabel, Genome-wide semi-automated annotation of transporter systems. IEEE-ACM Transactions on Computational Biology and Bioinformatics, 14(2), 443-456, 2017por
dc.identifier.issn15455963por
dc.identifier.urihttp://hdl.handle.net/1822/46349-
dc.description.abstractUsually, transport reactions are added to genome-scale metabolic models (GSMMs) based on experimental data and literature. This approach does not allow associating specific genes with transport reactions, which impairs the ability of the model to predict effects of gene deletions. Novel methods for systematic genome-wide transporter functional annotation and their integration into GSMMs are therefore necessary. In this work, an automatic system to detect and classify all potential membrane transport proteins for a given genome and integrate the related reactions into GSMMs is proposed, based on the identification and classification of genes that encode transmembrane proteins. The Transport Reactions Annotation and Generation (TRIAGE) tool identifies the metabolites transported by each transmembrane protein and its transporter family. The localization of the carriers is also predicted and, consequently, their action is confined to a given membrane. The integration of the data provided by TRIAGE with highly curated models allowed the identification of new transport reactions. TRIAGE is included in the new release of merlin, a software tool previously developed by the authors, which expedites the GSMM reconstruction processes.por
dc.description.sponsorshipThis work was partially supported by a PhD grant (SFRH /BD/47307/2008) and by the ERDF—European Regional Development Fund through the COMPETE Programme (operational programme for competitiveness), and National Funds through the FCT within the projects FCOMP-01-0124-FEDER-009707 (HeliSysBio—molecular Systems Biology in Helicobacter pylori) and PTDC/EIAEIA/115176/2009. The authors would also like to thank the FCT Strategic Project PEst-OE/EQB/LA0023/2013 and the Projects “BioInd - Biotechnology and Bioengineering for improved Industrial and Agro-Food processes”, REF. NORTE-07-0124-FEDER-000028 and “PEM – Metabolic Engineering Platform”, project number 23060 , both cofunded by the Programa Operacional Regional do Norte (ON.2 – O Novo Norte), QREN, FEDER.por
dc.language.isoengpor
dc.publisherIEEEpor
dc.relationinfo:eu-repo/grantAgreement/FCT/SFRH/SFRH%2FBD%2F47307%2F2008/PTpor
dc.relationinfo:eu-repo/grantAgreement/FCT/5876-PPCDTI/115176/PTpor
dc.relationinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/132966/PTpor
dc.rightsopenAccesspor
dc.subjectBioinformaticspor
dc.subjectBiological system modelingpor
dc.subjectBiomembranespor
dc.subjectDatabasespor
dc.subjectGenomicspor
dc.subjectOrganismspor
dc.subjectProteinspor
dc.subjectBioinformaticspor
dc.subjectGenome Transporters Inferencepor
dc.subjectGenome-scale metabolic modelspor
dc.subjectSystems Biologypor
dc.subjectTRIAGEpor
dc.subjectTransport Reactionspor
dc.subjectmerlinpor
dc.titleGenome-wide semi-automated annotation of transporter systemspor
dc.typearticle-
dc.peerreviewedyespor
dc.relation.publisherversionhttp://ieeexplore.ieee.org/xpl/RecentIssue.jsp?punumber=8857por
dc.commentsCEB37816por
degois.publication.firstPage443por
degois.publication.lastPage456por
degois.publication.issue2por
degois.publication.locationUnited States-
degois.publication.volume14por
dc.date.updated2017-08-03T11:01:32Z-
dc.identifier.essn1557-9964por
dc.identifier.doi10.1109/TCBB.2016.2527647por
dc.description.publicationversioninfo:eu-repo/semantics/publishedVersionpor
sdum.journalIEEE-ACM Transactions on Computational Biology and Bioinformaticspor
Aparece nas coleções:CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series

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