Genome-wide semi-automated annotation of transporter systems
Autor(a) principal: | |
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Data de Publicação: | 2017 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/1822/46349 |
Resumo: | Usually, 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. |
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Genome-wide semi-automated annotation of transporter systemsBioinformaticsBiological system modelingBiomembranesDatabasesGenomicsOrganismsProteinsBioinformaticsGenome Transporters InferenceGenome-scale metabolic modelsSystems BiologyTRIAGETransport ReactionsmerlinScience & TechnologyUsually, 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.This 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.info:eu-repo/semantics/publishedVersionIEEEUniversidade do MinhoDias, OscarGomes, Daniel G.Vilaça, P.Cardoso, JoãoRocha, MiguelFerreira, Eugénio C.Rocha, Isabel20172017-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/46349engDias, 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, 2017154559631557-996410.1109/TCBB.2016.252764726887005http://ieeexplore.ieee.org/xpl/RecentIssue.jsp?punumber=8857info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:18:55Zoai:repositorium.sdum.uminho.pt:1822/46349Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:11:46.584148Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Genome-wide semi-automated annotation of transporter systems |
title |
Genome-wide semi-automated annotation of transporter systems |
spellingShingle |
Genome-wide semi-automated annotation of transporter systems Dias, Oscar Bioinformatics Biological system modeling Biomembranes Databases Genomics Organisms Proteins Bioinformatics Genome Transporters Inference Genome-scale metabolic models Systems Biology TRIAGE Transport Reactions merlin Science & Technology |
title_short |
Genome-wide semi-automated annotation of transporter systems |
title_full |
Genome-wide semi-automated annotation of transporter systems |
title_fullStr |
Genome-wide semi-automated annotation of transporter systems |
title_full_unstemmed |
Genome-wide semi-automated annotation of transporter systems |
title_sort |
Genome-wide semi-automated annotation of transporter systems |
author |
Dias, Oscar |
author_facet |
Dias, Oscar Gomes, Daniel G. Vilaça, P. Cardoso, João Rocha, Miguel Ferreira, Eugénio C. Rocha, Isabel |
author_role |
author |
author2 |
Gomes, Daniel G. Vilaça, P. Cardoso, João Rocha, Miguel Ferreira, Eugénio C. Rocha, Isabel |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Dias, Oscar Gomes, Daniel G. Vilaça, P. Cardoso, João Rocha, Miguel Ferreira, Eugénio C. Rocha, Isabel |
dc.subject.por.fl_str_mv |
Bioinformatics Biological system modeling Biomembranes Databases Genomics Organisms Proteins Bioinformatics Genome Transporters Inference Genome-scale metabolic models Systems Biology TRIAGE Transport Reactions merlin Science & Technology |
topic |
Bioinformatics Biological system modeling Biomembranes Databases Genomics Organisms Proteins Bioinformatics Genome Transporters Inference Genome-scale metabolic models Systems Biology TRIAGE Transport Reactions merlin Science & Technology |
description |
Usually, 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. |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017 2017-01-01T00:00:00Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/1822/46349 |
url |
http://hdl.handle.net/1822/46349 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Dias, 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, 2017 15455963 1557-9964 10.1109/TCBB.2016.2527647 26887005 http://ieeexplore.ieee.org/xpl/RecentIssue.jsp?punumber=8857 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
IEEE |
publisher.none.fl_str_mv |
IEEE |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
instname_str |
Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
instacron_str |
RCAAP |
institution |
RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
collection |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository.name.fl_str_mv |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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1799132550634930176 |