An updated gene regulatory network reconstruction of multidrug-resistant Pseudomonas aeruginosa CCBH4851
Autor(a) principal: | |
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Data de Publicação: | 2022 |
Outros Autores: | , , , , |
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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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. |
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reponame:Repositório Institucional da FIOCRUZ (ARCA) instname:Fundação Oswaldo Cruz (FIOCRUZ) instacron:FIOCRUZ |
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Repositório Institucional da FIOCRUZ (ARCA) |
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