Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa [preprint]

Detalhes bibliográficos
Autor(a) principal: Medeiros Filho, Fernando
Data de Publicação: 2019
Outros Autores: Nascimento, Ana Paula Barbosa do, Santos, Marcelo Trindade dos, 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/33768
Resumo: Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Rio de Janeiro, RJ, Brasil.
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spelling Medeiros Filho, FernandoNascimento, Ana Paula Barbosa doSantos, Marcelo Trindade dosCarvalho-Assef, Ana Paula D’AlincourtSilva, Fabricio Alves Barbosa da2019-07-02T12:28:11Z2019-07-02T12:28:11Z2019MEDEIROS FILHO, Fernando et al. Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa. Memórias do Instituto Oswaldo Cruz, Rio de Janeiro, v. 114, p. 1-38, June 2019.0074-0276https://www.arca.fiocruz.br/handle/icict/3376810.1101/610493enghttps://www.arca.fiocruz.br/handle/icict/34303Pseudomonas aeruginosaRede reguladora de genesMúltiplos farmacosAnálisePseudomonas aeruginosaMultidrug-resistantGene regulatory networkAnalysisGene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa [preprint]info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Rio de Janeiro, RJ, Brasil.Laboratório Nacional de Computação Científica. Petrópolis, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Laboratório de Pesquisa em Infecção Hospitalar. Rio de Janeiro, RJ. Brasil.Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Rio de Janeiro, RJ, Brasil.BACKGROUND Healthcare-associated infections caused by bacteria such as Pseudomonas aeruginosa are a major public health problem worldwide. Gene regulatory networks computationally represent interactions among regulatory genes and their targets, an important approach to understand bacterial behavior and to provide novel ways of overcoming scientific challenges, including the identification of potential therapeutic targets and the development of new drugs. OBJECTIVES Our goal in this manuscript is to present a reconstruction of multidrug-resistant P. aeruginosa gene regulatory network and to analyze its topological properties. METHODS The methodology was based on gene orthology inference by the reciprocal best hit method. We used the genome of P. aeruginosa CCBH4851 as the basis of the reconstruction process. This multidrug-resistant strain is representative of an endemic outbreak in Brazilian territory belonging to ST277. FINDINGS As the main finding, we obtained a network with a larger number of regulatory genes, target genes and interactions compared to previous work. Topological analysis results are accordant to the complex network representation of biological processes. MAIN CONCLUSIONS The network properties are consistent with P. aeruginosa biological features. To the best of our knowledge, the P. aeruginosa gene regulatory network presented here is the most complete version available to date.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/33768/1/license.txt5a560609d32a3863062d77ff32785d58MD51ORIGINALAnaPaula_DAlincourt_etal_preprint_IOC_2019.pdfAnaPaula_DAlincourt_etal_preprint_IOC_2019.pdfapplication/pdf408506https://www.arca.fiocruz.br/bitstream/icict/33768/2/AnaPaula_DAlincourt_etal_preprint_IOC_2019.pdf2c8213f38633e3e694297f49fb1dc5a0MD52TEXTAnaPaula_DAlincourt_etal_preprint_IOC_2019.pdf.txtAnaPaula_DAlincourt_etal_preprint_IOC_2019.pdf.txtExtracted texttext/plain53569https://www.arca.fiocruz.br/bitstream/icict/33768/3/AnaPaula_DAlincourt_etal_preprint_IOC_2019.pdf.txt57c1c634e675c17274bbd836aeb698cfMD53icict/337682019-07-22 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dc.title.pt_BR.fl_str_mv Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa [preprint]
title Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa [preprint]
spellingShingle Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa [preprint]
Medeiros Filho, Fernando
Pseudomonas aeruginosa
Rede reguladora de genes
Múltiplos farmacos
Análise
Pseudomonas aeruginosa
Multidrug-resistant
Gene regulatory network
Analysis
title_short Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa [preprint]
title_full Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa [preprint]
title_fullStr Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa [preprint]
title_full_unstemmed Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa [preprint]
title_sort Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa [preprint]
author Medeiros Filho, Fernando
author_facet Medeiros Filho, Fernando
Nascimento, Ana Paula Barbosa do
Santos, Marcelo Trindade dos
Carvalho-Assef, Ana Paula D’Alincourt
Silva, Fabricio Alves Barbosa da
author_role author
author2 Nascimento, Ana Paula Barbosa do
Santos, Marcelo Trindade dos
Carvalho-Assef, Ana Paula D’Alincourt
Silva, Fabricio Alves Barbosa da
author2_role author
author
author
author
dc.contributor.author.fl_str_mv Medeiros Filho, Fernando
Nascimento, Ana Paula Barbosa do
Santos, Marcelo Trindade dos
Carvalho-Assef, Ana Paula D’Alincourt
Silva, Fabricio Alves Barbosa da
dc.subject.other.pt_BR.fl_str_mv Pseudomonas aeruginosa
Rede reguladora de genes
Múltiplos farmacos
Análise
topic Pseudomonas aeruginosa
Rede reguladora de genes
Múltiplos farmacos
Análise
Pseudomonas aeruginosa
Multidrug-resistant
Gene regulatory network
Analysis
dc.subject.en.pt_BR.fl_str_mv Pseudomonas aeruginosa
Multidrug-resistant
Gene regulatory network
Analysis
description Fundação Oswaldo Cruz. Presidência. Programa de Computação Científica. Rio de Janeiro, RJ, Brasil.
publishDate 2019
dc.date.accessioned.fl_str_mv 2019-07-02T12:28:11Z
dc.date.available.fl_str_mv 2019-07-02T12:28:11Z
dc.date.issued.fl_str_mv 2019
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 MEDEIROS FILHO, Fernando et al. Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa. Memórias do Instituto Oswaldo Cruz, Rio de Janeiro, v. 114, p. 1-38, June 2019.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/33768
dc.identifier.issn.pt_BR.fl_str_mv 0074-0276
dc.identifier.doi.pt_BR.fl_str_mv 10.1101/610493
identifier_str_mv MEDEIROS FILHO, Fernando et al. Gene regulatory network inference and analysis of multidrug-resistant Pseudomonas aeruginosa. Memórias do Instituto Oswaldo Cruz, Rio de Janeiro, v. 114, p. 1-38, June 2019.
0074-0276
10.1101/610493
url https://www.arca.fiocruz.br/handle/icict/33768
dc.language.iso.fl_str_mv eng
language eng
dc.relation.uri.pt_BR.fl_str_mv https://www.arca.fiocruz.br/handle/icict/34303
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
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
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collection Repositório Institucional da FIOCRUZ (ARCA)
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