Topological transitions on protein-protein interaction networks
Autor(a) principal: | |
---|---|
Data de Publicação: | 2019 |
Tipo de documento: | Tese |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UFPE |
Texto Completo: | https://repositorio.ufpe.br/handle/123456789/34186 |
Resumo: | In this work, we utilized concepts of applied algebraic topology to explore the very recent ideas of topological phase transitions in complex networks to the context of the Duplication Divergence model for protein-protein interaction Network. To do so, we used methods of topological data analysis to compute the Euler characteristic analytically, and the Betti numbers numerically for two variants of the Duplication Divergence model, namely the totally asymmetric model and the heterodimerization model. We contrast our theoretical results with experimental data freely available at online repositories of gene coexpression networks of Saccharomyces cerevisiae, also known as baker’s yeast, as well as of the nematode Caenorhabditis elegans. We detected one topological phase transition in Yeast networks obtained according to different similarity measures, corresponding to phase transitions at close critical thresholds. Our results give evidence that the Euler characteristic can be interpreted as an intrinsic bio-marker for Yeast networks and reinforces the hypothesis of the possibility of using topological phase transitions to build topological and geometrical biomarkers for networks more generally. |
id |
UFPE_2fb28668bac71ffdb926a29ab30c1eeb |
---|---|
oai_identifier_str |
oai:repositorio.ufpe.br:123456789/34186 |
network_acronym_str |
UFPE |
network_name_str |
Repositório Institucional da UFPE |
repository_id_str |
2221 |
spelling |
AMORIM FILHO, Edgar Corrêa dehttp://lattes.cnpq.br/0697314354160472http://lattes.cnpq.br/9100032882367430SANTOS, Fernando Antônio Nóbrega2019-10-04T17:48:11Z2019-10-04T17:48:11Z2019-02-25https://repositorio.ufpe.br/handle/123456789/34186In this work, we utilized concepts of applied algebraic topology to explore the very recent ideas of topological phase transitions in complex networks to the context of the Duplication Divergence model for protein-protein interaction Network. To do so, we used methods of topological data analysis to compute the Euler characteristic analytically, and the Betti numbers numerically for two variants of the Duplication Divergence model, namely the totally asymmetric model and the heterodimerization model. We contrast our theoretical results with experimental data freely available at online repositories of gene coexpression networks of Saccharomyces cerevisiae, also known as baker’s yeast, as well as of the nematode Caenorhabditis elegans. We detected one topological phase transition in Yeast networks obtained according to different similarity measures, corresponding to phase transitions at close critical thresholds. Our results give evidence that the Euler characteristic can be interpreted as an intrinsic bio-marker for Yeast networks and reinforces the hypothesis of the possibility of using topological phase transitions to build topological and geometrical biomarkers for networks more generally.CAPESCNPqNeste trabalho, utilizamos métodos de topologia algébrica aplicada para explorar o recente conceito de transições de fase topológicas em redes complexas em modelos de interação entre proteínas. Em particular, usamos métodos de análise topológica de dados para computar analiticamente a característica de Euler e numericamente os números de Betti para duas variações do modelo de Duplicação e Divergência em redes de interação entre proteínas, a saber, o modelo totalmente assimétrico e o modelo com heterodimerização. Contrastamos nossos resultados teóricos e numéricos com dados experimentais disponíveis em repositórios online para redes de coexpressão genética da Saccharomyces cerevisiae, a levedura utilizada na produção do pão e de cerveja, bem como para o nematoide Caenorhabditis elegans. Detectamos uma transição de fase nas redes de levedura, obtidas através de diferentes medidas de similaridade, que corresponde a transições de fase em um valor de correlação crítica com poucas flutuações. Nosso resultado dá evidências de que a característica de Euler pode ser interpretada como biomarcador intrínseco para redes de interação entre proteínas e reitera a possibilidade de utilizar transições de fase topológicas para construir biomarcadores topológicos e geométricos em redes de uma maneira geral.engUniversidade Federal de PernambucoPrograma de Pos Graduacao em MatematicaUFPEBrasilAttribution-NonCommercial-NoDerivs 3.0 Brazilhttp://creativecommons.org/licenses/by-nc-nd/3.0/br/info:eu-repo/semantics/openAccessMatemáticaCaracterística de EulerTopological transitions on protein-protein interaction networksinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/doctoralThesisdoutoradoreponame:Repositório Institucional da UFPEinstname:Universidade Federal de Pernambuco (UFPE)instacron:UFPETHUMBNAILTESE Edgar Corrêa de Amorim Filho.pdf.jpgTESE Edgar Corrêa de Amorim Filho.pdf.jpgGenerated Thumbnailimage/jpeg1211https://repositorio.ufpe.br/bitstream/123456789/34186/5/TESE%20Edgar%20Corr%c3%aaa%20de%20Amorim%20Filho.pdf.jpgf9a39a4dfc09cf0a5ca92a7ba9f7deceMD55ORIGINALTESE Edgar Corrêa de Amorim Filho.pdfTESE Edgar Corrêa de Amorim Filho.pdfapplication/pdf4165374https://repositorio.ufpe.br/bitstream/123456789/34186/1/TESE%20Edgar%20Corr%c3%aaa%20de%20Amorim%20Filho.pdf770c5925da23ddf582e918462da350aeMD51CC-LICENSElicense_rdflicense_rdfapplication/rdf+xml; charset=utf-8811https://repositorio.ufpe.br/bitstream/123456789/34186/2/license_rdfe39d27027a6cc9cb039ad269a5db8e34MD52LICENSElicense.txtlicense.txttext/plain; charset=utf-82310https://repositorio.ufpe.br/bitstream/123456789/34186/3/license.txtbd573a5ca8288eb7272482765f819534MD53TEXTTESE Edgar Corrêa de Amorim Filho.pdf.txtTESE Edgar Corrêa de Amorim Filho.pdf.txtExtracted texttext/plain106812https://repositorio.ufpe.br/bitstream/123456789/34186/4/TESE%20Edgar%20Corr%c3%aaa%20de%20Amorim%20Filho.pdf.txt701363433e3fa84953ed39b7494cda60MD54123456789/341862019-10-25 11:00:15.023oai:repositorio.ufpe.br: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ório InstitucionalPUBhttps://repositorio.ufpe.br/oai/requestattena@ufpe.bropendoar:22212019-10-25T14:00:15Repositório Institucional da UFPE - Universidade Federal de Pernambuco (UFPE)false |
dc.title.pt_BR.fl_str_mv |
Topological transitions on protein-protein interaction networks |
title |
Topological transitions on protein-protein interaction networks |
spellingShingle |
Topological transitions on protein-protein interaction networks AMORIM FILHO, Edgar Corrêa de Matemática Característica de Euler |
title_short |
Topological transitions on protein-protein interaction networks |
title_full |
Topological transitions on protein-protein interaction networks |
title_fullStr |
Topological transitions on protein-protein interaction networks |
title_full_unstemmed |
Topological transitions on protein-protein interaction networks |
title_sort |
Topological transitions on protein-protein interaction networks |
author |
AMORIM FILHO, Edgar Corrêa de |
author_facet |
AMORIM FILHO, Edgar Corrêa de |
author_role |
author |
dc.contributor.authorLattes.pt_BR.fl_str_mv |
http://lattes.cnpq.br/0697314354160472 |
dc.contributor.advisorLattes.pt_BR.fl_str_mv |
http://lattes.cnpq.br/9100032882367430 |
dc.contributor.author.fl_str_mv |
AMORIM FILHO, Edgar Corrêa de |
dc.contributor.advisor1.fl_str_mv |
SANTOS, Fernando Antônio Nóbrega |
contributor_str_mv |
SANTOS, Fernando Antônio Nóbrega |
dc.subject.por.fl_str_mv |
Matemática Característica de Euler |
topic |
Matemática Característica de Euler |
description |
In this work, we utilized concepts of applied algebraic topology to explore the very recent ideas of topological phase transitions in complex networks to the context of the Duplication Divergence model for protein-protein interaction Network. To do so, we used methods of topological data analysis to compute the Euler characteristic analytically, and the Betti numbers numerically for two variants of the Duplication Divergence model, namely the totally asymmetric model and the heterodimerization model. We contrast our theoretical results with experimental data freely available at online repositories of gene coexpression networks of Saccharomyces cerevisiae, also known as baker’s yeast, as well as of the nematode Caenorhabditis elegans. We detected one topological phase transition in Yeast networks obtained according to different similarity measures, corresponding to phase transitions at close critical thresholds. Our results give evidence that the Euler characteristic can be interpreted as an intrinsic bio-marker for Yeast networks and reinforces the hypothesis of the possibility of using topological phase transitions to build topological and geometrical biomarkers for networks more generally. |
publishDate |
2019 |
dc.date.accessioned.fl_str_mv |
2019-10-04T17:48:11Z |
dc.date.available.fl_str_mv |
2019-10-04T17:48:11Z |
dc.date.issued.fl_str_mv |
2019-02-25 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/doctoralThesis |
format |
doctoralThesis |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
https://repositorio.ufpe.br/handle/123456789/34186 |
url |
https://repositorio.ufpe.br/handle/123456789/34186 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
Attribution-NonCommercial-NoDerivs 3.0 Brazil http://creativecommons.org/licenses/by-nc-nd/3.0/br/ info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
Attribution-NonCommercial-NoDerivs 3.0 Brazil http://creativecommons.org/licenses/by-nc-nd/3.0/br/ |
eu_rights_str_mv |
openAccess |
dc.publisher.none.fl_str_mv |
Universidade Federal de Pernambuco |
dc.publisher.program.fl_str_mv |
Programa de Pos Graduacao em Matematica |
dc.publisher.initials.fl_str_mv |
UFPE |
dc.publisher.country.fl_str_mv |
Brasil |
publisher.none.fl_str_mv |
Universidade Federal de Pernambuco |
dc.source.none.fl_str_mv |
reponame:Repositório Institucional da UFPE instname:Universidade Federal de Pernambuco (UFPE) instacron:UFPE |
instname_str |
Universidade Federal de Pernambuco (UFPE) |
instacron_str |
UFPE |
institution |
UFPE |
reponame_str |
Repositório Institucional da UFPE |
collection |
Repositório Institucional da UFPE |
bitstream.url.fl_str_mv |
https://repositorio.ufpe.br/bitstream/123456789/34186/5/TESE%20Edgar%20Corr%c3%aaa%20de%20Amorim%20Filho.pdf.jpg https://repositorio.ufpe.br/bitstream/123456789/34186/1/TESE%20Edgar%20Corr%c3%aaa%20de%20Amorim%20Filho.pdf https://repositorio.ufpe.br/bitstream/123456789/34186/2/license_rdf https://repositorio.ufpe.br/bitstream/123456789/34186/3/license.txt https://repositorio.ufpe.br/bitstream/123456789/34186/4/TESE%20Edgar%20Corr%c3%aaa%20de%20Amorim%20Filho.pdf.txt |
bitstream.checksum.fl_str_mv |
f9a39a4dfc09cf0a5ca92a7ba9f7dece 770c5925da23ddf582e918462da350ae e39d27027a6cc9cb039ad269a5db8e34 bd573a5ca8288eb7272482765f819534 701363433e3fa84953ed39b7494cda60 |
bitstream.checksumAlgorithm.fl_str_mv |
MD5 MD5 MD5 MD5 MD5 |
repository.name.fl_str_mv |
Repositório Institucional da UFPE - Universidade Federal de Pernambuco (UFPE) |
repository.mail.fl_str_mv |
attena@ufpe.br |
_version_ |
1802310699871895552 |