Detecting Network Communities: An Application to Phylogenetic Analysis

Detalhes bibliográficos
Autor(a) principal: Andrade, Roberto Fernandes Silva
Data de Publicação: 2011
Outros Autores: Rocha Neto, Ivan C., Santos, Leonardo B. L., Santana, Charles N. de, Diniz, Marcelo V. C., Lobão, Thierry Corrêa Petit, Goés Neto, Aristóteles, Pinho, Suani Tavares Rubim de, El-Hani, Charbel Niño
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UFBA
Texto Completo: http://www.repositorio.ufba.br/ri/handle/ri/5419
Resumo: p. 13
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spelling Andrade, Roberto Fernandes SilvaRocha Neto, Ivan C.Santos, Leonardo B. L.Santana, Charles N. deDiniz, Marcelo V. C.Lobão, Thierry Corrêa PetitGoés Neto, AristótelesPinho, Suani Tavares Rubim deEl-Hani, Charbel NiñoAndrade, Roberto Fernandes SilvaRocha Neto, Ivan C.Santos, Leonardo B. L.Santana, Charles N. deDiniz, Marcelo V. C.Lobão, Thierry Corrêa PetitGoés Neto, AristótelesPinho, Suani Tavares Rubim deEl-Hani, Charbel Niño2012-02-14T13:12:25Z2012-02-14T13:12:25Z2011ISSN: 1553-734Xhttp://www.repositorio.ufba.br/ri/handle/ri/5419v. 7, n. 5.p. 13This paper proposes a new method to identify communities in generally weighted complex networks and apply it to phylogenetic analysis. In this case, weights correspond to the similarity indexes among protein sequences, which can be used for network construction so that the network structure can be analyzed to recover phylogenetically useful information from its properties. The analyses discussed here are mainly based on the modular character of protein similarity networks, explored through the Newman-Girvan algorithm, with the help of the neighborhood matrix Mˆ . The most relevant networks are found when the network topology changes abruptly revealing distinct modules related to the sets of organisms to which the proteins belong. Sound biological information can be retrieved by the computational routines used in the network approach, without using biological assumptions other than those incorporated by BLAST. Usually, all the main bacterial phyla and, in some cases, also some bacterial classes corresponded totally (100%) or to a great extent (.70%) to the modules. We checked for internal consistency in the obtained results, and we scored close to 84% of matches for community pertinence when comparisons between the results were performed. To illustrate how to use the network-based method, we employed data for enzymes involved in the chitin metabolic pathway that are present in more than 100 organisms from an original data set containing 1,695 organisms, downloaded from GenBank on May 19, 2007. A preliminary comparison between the outcomes of the network-based method and the results of methods based on Bayesian, distance, likelihood, and parsimony criteria suggests that the former is as reliable as these commonly used methods. We conclude that the network-based method can be used as a powerful tool for retrieving modularity information from weighted networks, which is useful for phylogenetic analysis.Submitted by JURANDI DE SOUZA SILVA (jssufba@hotmail.com) on 2012-02-14T13:12:25Z No. of bitstreams: 1 journal.pcbi.1001131.pdf: 618605 bytes, checksum: 54da2471f0b1aa746472042e6e3679b6 (MD5)Made available in DSpace on 2012-02-14T13:12:25Z (GMT). No. of bitstreams: 1 journal.pcbi.1001131.pdf: 618605 bytes, checksum: 54da2471f0b1aa746472042e6e3679b6 (MD5) Previous issue date: 2011DOI: 10.1371/journal.pcbi.1001131reponame:Repositório Institucional da UFBAinstname:Universidade Federal da Bahia (UFBA)instacron:UFBADetecting Network Communities: An Application to Phylogenetic AnalysisPLoS Computational Biologyinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleenginfo:eu-repo/semantics/openAccessORIGINALjournal.pcbi.1001131.pdfjournal.pcbi.1001131.pdfapplication/pdf618605https://repositorio.ufba.br/bitstream/ri/5419/1/journal.pcbi.1001131.pdf54da2471f0b1aa746472042e6e3679b6MD51LICENSElicense.txtlicense.txttext/plain1762https://repositorio.ufba.br/bitstream/ri/5419/2/license.txt1b89a9a0548218172d7c829f87a0eab9MD52TEXTjournal.pcbi.1001131.pdf.txtjournal.pcbi.1001131.pdf.txtExtracted texttext/plain74323https://repositorio.ufba.br/bitstream/ri/5419/3/journal.pcbi.1001131.pdf.txt83101f95208d5bc7778193754d52a3d8MD53ri/54192022-07-05 14:03:48.053oai:repositorio.ufba.br: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Repositório InstitucionalPUBhttp://192.188.11.11:8080/oai/requestopendoar:19322022-07-05T17:03:48Repositório Institucional da UFBA - Universidade Federal da Bahia (UFBA)false
dc.title.pt_BR.fl_str_mv Detecting Network Communities: An Application to Phylogenetic Analysis
dc.title.alternative.pt_BR.fl_str_mv PLoS Computational Biology
title Detecting Network Communities: An Application to Phylogenetic Analysis
spellingShingle Detecting Network Communities: An Application to Phylogenetic Analysis
Andrade, Roberto Fernandes Silva
title_short Detecting Network Communities: An Application to Phylogenetic Analysis
title_full Detecting Network Communities: An Application to Phylogenetic Analysis
title_fullStr Detecting Network Communities: An Application to Phylogenetic Analysis
title_full_unstemmed Detecting Network Communities: An Application to Phylogenetic Analysis
title_sort Detecting Network Communities: An Application to Phylogenetic Analysis
author Andrade, Roberto Fernandes Silva
author_facet Andrade, Roberto Fernandes Silva
Rocha Neto, Ivan C.
Santos, Leonardo B. L.
Santana, Charles N. de
Diniz, Marcelo V. C.
Lobão, Thierry Corrêa Petit
Goés Neto, Aristóteles
Pinho, Suani Tavares Rubim de
El-Hani, Charbel Niño
author_role author
author2 Rocha Neto, Ivan C.
Santos, Leonardo B. L.
Santana, Charles N. de
Diniz, Marcelo V. C.
Lobão, Thierry Corrêa Petit
Goés Neto, Aristóteles
Pinho, Suani Tavares Rubim de
El-Hani, Charbel Niño
author2_role author
author
author
author
author
author
author
author
dc.contributor.author.fl_str_mv Andrade, Roberto Fernandes Silva
Rocha Neto, Ivan C.
Santos, Leonardo B. L.
Santana, Charles N. de
Diniz, Marcelo V. C.
Lobão, Thierry Corrêa Petit
Goés Neto, Aristóteles
Pinho, Suani Tavares Rubim de
El-Hani, Charbel Niño
Andrade, Roberto Fernandes Silva
Rocha Neto, Ivan C.
Santos, Leonardo B. L.
Santana, Charles N. de
Diniz, Marcelo V. C.
Lobão, Thierry Corrêa Petit
Goés Neto, Aristóteles
Pinho, Suani Tavares Rubim de
El-Hani, Charbel Niño
description p. 13
publishDate 2011
dc.date.issued.fl_str_mv 2011
dc.date.accessioned.fl_str_mv 2012-02-14T13:12:25Z
dc.date.available.fl_str_mv 2012-02-14T13:12:25Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
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status_str publishedVersion
dc.identifier.uri.fl_str_mv http://www.repositorio.ufba.br/ri/handle/ri/5419
dc.identifier.issn.none.fl_str_mv ISSN: 1553-734X
dc.identifier.number.pt_BR.fl_str_mv v. 7, n. 5.
identifier_str_mv ISSN: 1553-734X
v. 7, n. 5.
url http://www.repositorio.ufba.br/ri/handle/ri/5419
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.pt_BR.fl_str_mv DOI: 10.1371/journal.pcbi.1001131
dc.source.none.fl_str_mv reponame:Repositório Institucional da UFBA
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