An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851

Detalhes bibliográficos
Autor(a) principal: Chagas, Márcia da Silva
Data de Publicação: 2022
Outros Autores: Medeiros Filho, Fernando, Santos, Marcelo Trindade dos, Menezes, Marcio Argollo de, Carvalho-Assef, Ana Paula D’Alincourt, Silva, Fabricio Alves Barbosa da
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/57034
Resumo: Fundação Oswaldo Cruz-Fiocruz. Programa de Computação Científica, Rio de Janeiro, RJ, Brasil.
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spelling Chagas, Márcia da SilvaMedeiros Filho, FernandoSantos, Marcelo Trindade dosMenezes, Marcio Argollo deCarvalho-Assef, Ana Paula D’AlincourtSilva, Fabricio Alves Barbosa da2023-02-13T15:08:28Z2023-02-13T15:08:28Z2022CHAGAS, Márcia da Silva et al. An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851. Memórias do Instituto Oswaldo Cruz, Rio de Janeiro, v. 117: e220111, p. 1 - 15, 2022.0074-0206https://www.arca.fiocruz.br/handle/icict/5703410.1590/0074-02760220111engFundação Oswaldo Cruz. Instituto Oswaldo Cruz.Pseudomonas aeruginosaRede reguladora de genesResistência a múltiplas drogasBiologia do sistemaPseudomonas aeruginosaGene regulatory networkMultidrug resistanceSystem biologyAn updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz-Fiocruz. Programa de Computação Científica, Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Nacional de Infectologia, Laboratório de Pesquisa Clínica em Doenças Febris Agudas, Rio de Janeiro, RJ, Brasil.Laboratório Nacional de Computação Científica. Petrópolis, RJ, Brasil.Universidade Federal Fluminense. Instituto de Física, Niterói, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Pesquisa em Infecção Hospitalar. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz-Fiocruz. Programa de Computação Científica, Rio de Janeiro, RJ, Brasil.BACKGROUND Healthcare-associated infections due to multidrug-resistant (MDR) bacteria such as Pseudomonas aeruginosa are significant public health issues worldwide. A system biology approach can help understand bacterial behaviour and provide novel ways to identify potential therapeutic targets and develop new drugs. Gene regulatory networks (GRN) are examples of in silico representation of interaction between regulatory genes and their targets. OBJECTIVES In this work, we update the MDR P. aeruginosa CCBH4851 GRN reconstruction and analyse and discuss its structural properties. METHODS We based this study on the gene orthology inference methodology using the reciprocal best hit method. The P. aeruginosa CCBH4851 genome and GRN, published in 2019, and the P. aeruginosa PAO1 GRN, published in 2020, were used for this update reconstruction process. FINDINGS Our result is a GRN with a greater number of regulatory genes, target genes, and interactions compared to the previous networks, and its structural properties are consistent with the complexity of biological networks and the biological features of P. aeruginosa. MAIN CONCLUSIONS Here, we present the largest and most complete version of P. aeruginosa GRN published to this date, to the best of our knowledge.info:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZLICENSElicense.txtlicense.txttext/plain; charset=utf-82991https://www.arca.fiocruz.br/bitstream/icict/57034/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALAnaPaulaAssef_etal_IOC_2022.pdfAnaPaulaAssef_etal_IOC_2022.pdfapplication/pdf3668354https://www.arca.fiocruz.br/bitstream/icict/57034/2/AnaPaulaAssef_etal_IOC_2022.pdf2fed52c81d89bfd75349e13cd3bc9ed5MD52icict/570342023-09-04 11:29:52.501oai:www.arca.fiocruz.br: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ório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-09-04T14:29:52Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.en_US.fl_str_mv An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851
title An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851
spellingShingle An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851
Chagas, Márcia da Silva
Pseudomonas aeruginosa
Rede reguladora de genes
Resistência a múltiplas drogas
Biologia do sistema
Pseudomonas aeruginosa
Gene regulatory network
Multidrug resistance
System biology
title_short An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851
title_full An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851
title_fullStr An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851
title_full_unstemmed An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851
title_sort An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851
author Chagas, Márcia da Silva
author_facet Chagas, Márcia da Silva
Medeiros Filho, Fernando
Santos, Marcelo Trindade dos
Menezes, Marcio Argollo de
Carvalho-Assef, Ana Paula D’Alincourt
Silva, Fabricio Alves Barbosa da
author_role author
author2 Medeiros Filho, Fernando
Santos, Marcelo Trindade dos
Menezes, Marcio Argollo de
Carvalho-Assef, Ana Paula D’Alincourt
Silva, Fabricio Alves Barbosa da
author2_role author
author
author
author
author
dc.contributor.author.fl_str_mv Chagas, Márcia da Silva
Medeiros Filho, Fernando
Santos, Marcelo Trindade dos
Menezes, Marcio Argollo de
Carvalho-Assef, Ana Paula D’Alincourt
Silva, Fabricio Alves Barbosa da
dc.subject.other.en_US.fl_str_mv Pseudomonas aeruginosa
Rede reguladora de genes
Resistência a múltiplas drogas
Biologia do sistema
topic Pseudomonas aeruginosa
Rede reguladora de genes
Resistência a múltiplas drogas
Biologia do sistema
Pseudomonas aeruginosa
Gene regulatory network
Multidrug resistance
System biology
dc.subject.en.en_US.fl_str_mv Pseudomonas aeruginosa
Gene regulatory network
Multidrug resistance
System biology
description Fundação Oswaldo Cruz-Fiocruz. Programa de Computação Científica, Rio de Janeiro, RJ, Brasil.
publishDate 2022
dc.date.issued.fl_str_mv 2022
dc.date.accessioned.fl_str_mv 2023-02-13T15:08:28Z
dc.date.available.fl_str_mv 2023-02-13T15:08:28Z
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.citation.fl_str_mv CHAGAS, Márcia da Silva et al. An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851. Memórias do Instituto Oswaldo Cruz, Rio de Janeiro, v. 117: e220111, p. 1 - 15, 2022.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/57034
dc.identifier.issn.en_US.fl_str_mv 0074-0206
dc.identifier.doi.none.fl_str_mv 10.1590/0074-02760220111
identifier_str_mv CHAGAS, Márcia da Silva et al. An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851. Memórias do Instituto Oswaldo Cruz, Rio de Janeiro, v. 117: e220111, p. 1 - 15, 2022.
0074-0206
10.1590/0074-02760220111
url https://www.arca.fiocruz.br/handle/icict/57034
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Fundação Oswaldo Cruz. Instituto Oswaldo Cruz.
publisher.none.fl_str_mv Fundação Oswaldo Cruz. Instituto Oswaldo Cruz.
dc.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
instacron_str FIOCRUZ
institution FIOCRUZ
reponame_str Repositório Institucional da FIOCRUZ (ARCA)
collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/57034/1/license.txt
https://www.arca.fiocruz.br/bitstream/icict/57034/2/AnaPaulaAssef_etal_IOC_2022.pdf
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repository.name.fl_str_mv Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)
repository.mail.fl_str_mv repositorio.arca@fiocruz.br
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