In silico predictions of protein interactions between Zika virus and human host

Detalhes bibliográficos
Autor(a) principal: Pitta, João Luiz de Lemos Padilha
Data de Publicação: 2021
Outros Autores: Vasconcelos, Crhisllane Rafaele Dos Santos, Wallau, Gabriel da Luz, Campos, Túlio de Lima, Rezende, Antonio Mauro
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da FIOCRUZ (ARCA)
Texto Completo: https://www.arca.fiocruz.br/handle/icict/58546
Resumo: Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Microbiology Department. Recife, PE, Brasil.
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spelling Pitta, João Luiz de Lemos PadilhaVasconcelos, Crhisllane Rafaele Dos SantosWallau, Gabriel da LuzCampos, Túlio de LimaRezende, Antonio Mauro2023-05-22T14:00:46Z2023-05-22T14:00:46Z2021PITTA, João Luiz de Lemos Padilha et al. In silico predictions of protein interactions between Zika virus and human host. Peerj, [S.l.], v. 9, p. 1-23, 24 ago. 2021. PeerJ.2167-8359https://www.arca.fiocruz.br/handle/icict/5854610.7717/peerj.117702167-8359engIn silico predictions of protein interactions between Zika virus and human hostinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleFundação Oswaldo Cruz. Instituto Aggeu Magalhães. Microbiology Department. Recife, PE, Brasil.Federal University of Pernambuco. Genetics Department. Recife, PE, Brasil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Entomology Department . Recife, PE, Brasil.Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Bioinformatics Platform. Recife, PE, Brasil.Background: The ZIKA virus (ZIKV) belongs to the Flaviviridae family, was first isolated in the 1940s, and remained underreported until its global threat in 2016, where drastic consequences were reported as Guillan-Barre syndrome and microcephaly in newborns. Understanding molecular interactions of ZIKV proteins during the host infection is important to develop treatments and prophylactic measures; however, large-scale experimental approaches normally used to detect protein-protein interaction (PPI) are onerous and labor-intensive. On the other hand, computational methods may overcome these challenges and guide traditional approaches on one or few protein molecules. The prediction of PPIs can be used to study host-parasite interactions at the protein level and reveal key pathways that allow viral infection. Results: Applying Random Forest and Support Vector Machine (SVM) algorithms, we performed predictions of PPI between two ZIKV strains and human proteomes. The consensus number of predictions of both algorithms was 17,223 pairs of proteins. Functional enrichment analyses were executed with the predicted networks to access the biological meanings of the protein interactions. Some pathways related to viral infection and neurological development were found for both ZIKV strains in the enrichment analysis, but the JAK-STAT pathway was observed only for strain PE243 when compared with the FSS13025 strain. Conclusions: The consensus network of PPI predictions made by Random Forest and SVM algorithms allowed an enrichment analysis that corroborates many aspects of ZIKV infection. The enrichment results are mainly related to viral infection, neuronal development, and immune response, and presented differences among the two compared ZIKV strains. Strain PE243 presented more predicted interactions between proteins from the JAK-STAT signaling pathway, which could lead to a more inflammatory immune response when compared with the FSS13025 strain. These results show that the methodology employed in this study can potentially reveal new interactions between the ZIKV and human cells.Machine learningMetabolic pathwayProtein-protein interactionsZika virusinfo:eu-repo/semantics/openAccessreponame:Repositório Institucional da FIOCRUZ (ARCA)instname:Fundação Oswaldo Cruz (FIOCRUZ)instacron:FIOCRUZORIGINALIn silico predictions of protein interactions between zika virus and human host.pdfIn silico predictions of protein interactions between zika virus and human host.pdfapplication/pdf5002611https://www.arca.fiocruz.br/bitstream/icict/58546/2/In%20silico%20predictions%20of%20protein%20interactions%20between%20zika%20virus%20and%20human%20host.pdf5f369d4ae17a8343f4fbce0bdb6615dcMD52LICENSElicense.txttext/plain1748https://www.arca.fiocruz.br/bitstream/icict/58546/1/license.txt8a4605be74aa9ea9d79846c1fba20a33MD51icict/585462023-05-22 11:00:47.538oai:www.arca.fiocruz.br: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Repositório InstitucionalPUBhttps://www.arca.fiocruz.br/oai/requestrepositorio.arca@fiocruz.bropendoar:21352023-05-22T14:00:47Repositório Institucional da FIOCRUZ (ARCA) - Fundação Oswaldo Cruz (FIOCRUZ)false
dc.title.en_US.fl_str_mv In silico predictions of protein interactions between Zika virus and human host
title In silico predictions of protein interactions between Zika virus and human host
spellingShingle In silico predictions of protein interactions between Zika virus and human host
Pitta, João Luiz de Lemos Padilha
Machine learning
Metabolic pathway
Protein-protein interactions
Zika virus
title_short In silico predictions of protein interactions between Zika virus and human host
title_full In silico predictions of protein interactions between Zika virus and human host
title_fullStr In silico predictions of protein interactions between Zika virus and human host
title_full_unstemmed In silico predictions of protein interactions between Zika virus and human host
title_sort In silico predictions of protein interactions between Zika virus and human host
author Pitta, João Luiz de Lemos Padilha
author_facet Pitta, João Luiz de Lemos Padilha
Vasconcelos, Crhisllane Rafaele Dos Santos
Wallau, Gabriel da Luz
Campos, Túlio de Lima
Rezende, Antonio Mauro
author_role author
author2 Vasconcelos, Crhisllane Rafaele Dos Santos
Wallau, Gabriel da Luz
Campos, Túlio de Lima
Rezende, Antonio Mauro
author2_role author
author
author
author
dc.contributor.author.fl_str_mv Pitta, João Luiz de Lemos Padilha
Vasconcelos, Crhisllane Rafaele Dos Santos
Wallau, Gabriel da Luz
Campos, Túlio de Lima
Rezende, Antonio Mauro
dc.subject.en.en_US.fl_str_mv Machine learning
Metabolic pathway
Protein-protein interactions
Zika virus
topic Machine learning
Metabolic pathway
Protein-protein interactions
Zika virus
description Fundação Oswaldo Cruz. Instituto Aggeu Magalhães. Microbiology Department. Recife, PE, Brasil.
publishDate 2021
dc.date.issued.fl_str_mv 2021
dc.date.accessioned.fl_str_mv 2023-05-22T14:00:46Z
dc.date.available.fl_str_mv 2023-05-22T14:00:46Z
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 PITTA, João Luiz de Lemos Padilha et al. In silico predictions of protein interactions between Zika virus and human host. Peerj, [S.l.], v. 9, p. 1-23, 24 ago. 2021. PeerJ.
dc.identifier.uri.fl_str_mv https://www.arca.fiocruz.br/handle/icict/58546
dc.identifier.issn.en_US.fl_str_mv 2167-8359
dc.identifier.doi.none.fl_str_mv 10.7717/peerj.11770
dc.identifier.eissn.none.fl_str_mv 2167-8359
identifier_str_mv PITTA, João Luiz de Lemos Padilha et al. In silico predictions of protein interactions between Zika virus and human host. Peerj, [S.l.], v. 9, p. 1-23, 24 ago. 2021. PeerJ.
2167-8359
10.7717/peerj.11770
url https://www.arca.fiocruz.br/handle/icict/58546
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.source.none.fl_str_mv reponame:Repositório Institucional da FIOCRUZ (ARCA)
instname:Fundação Oswaldo Cruz (FIOCRUZ)
instacron:FIOCRUZ
instname_str Fundação Oswaldo Cruz (FIOCRUZ)
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collection Repositório Institucional da FIOCRUZ (ARCA)
bitstream.url.fl_str_mv https://www.arca.fiocruz.br/bitstream/icict/58546/2/In%20silico%20predictions%20of%20protein%20interactions%20between%20zika%20virus%20and%20human%20host.pdf
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