A principal components method constrained by elementary flux modes

Detalhes bibliográficos
Autor(a) principal: von Stosch, Moritz
Data de Publicação: 2016
Outros Autores: de Azevedo, Cristiana Rodrigues, Luís, Mauro, de Azevedo, Sebastiao Feyo, Oliveira, Rui
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10362/154050
Resumo: Deutscher Akademischer Austausch Dienst, Reference number: 6818.
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spelling A principal components method constrained by elementary flux modesAnalysis of flux data setsElementary flux modesFlux data analysisFluxome data analysisPrincipal component analysisPrinciple elementary modesStructural BiologyBiochemistryMolecular BiologyComputer Science ApplicationsApplied MathematicsDeutscher Akademischer Austausch Dienst, Reference number: 6818.Background: Non-negative linear combinations of elementary flux modes (EMs) describe all feasible reaction flux distributions for a given metabolic network under the quasi steady state assumption. However, only a small subset of EMs contribute to the physiological state of a given cell. Results: In this paper, a method is proposed that identifies the subset of EMs that best explain the physiological state captured in reaction flux data, referred to as principal EMs (PEMs), given a pre-specified universe of EM candidates. The method avoids the evaluation of all possible combinations of EMs by using a branch and bound approach which is computationally very efficient. The performance of the method is assessed using simulated and experimental data of Pichia pastoris and experimental fluxome data of Saccharomyces cerevisiae. The proposed method is benchmarked against principal component analysis (PCA), commonly used to study the structure of metabolic flux data sets. Conclusions: The overall results show that the proposed method is computationally very effective in identifying the subset of PEMs within a large set of EM candidates (cases with ~100 and ~1000 EMs were studied). In contrast to the principal components in PCA, the identified PEMs have a biological meaning enabling identification of the key active pathways in a cell as well as the conditions under which the pathways are activated. This method clearly outperforms PCA in the interpretability of flux data providing additional insights into the underlying regulatory mechanisms.DQ - Departamento de QuímicaLAQV@REQUIMTERUNvon Stosch, Moritzde Azevedo, Cristiana RodriguesLuís, Maurode Azevedo, Sebastiao FeyoOliveira, Rui2023-06-16T22:17:03Z20162016-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article19application/pdfhttp://hdl.handle.net/10362/154050eng1471-2105PURE: 14322148https://doi.org/10.1186/s12859-016-1063-0info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T05:36:32Zoai:run.unl.pt:10362/154050Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:55:29.248392Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv A principal components method constrained by elementary flux modes
Analysis of flux data sets
title A principal components method constrained by elementary flux modes
spellingShingle A principal components method constrained by elementary flux modes
von Stosch, Moritz
Elementary flux modes
Flux data analysis
Fluxome data analysis
Principal component analysis
Principle elementary modes
Structural Biology
Biochemistry
Molecular Biology
Computer Science Applications
Applied Mathematics
title_short A principal components method constrained by elementary flux modes
title_full A principal components method constrained by elementary flux modes
title_fullStr A principal components method constrained by elementary flux modes
title_full_unstemmed A principal components method constrained by elementary flux modes
title_sort A principal components method constrained by elementary flux modes
author von Stosch, Moritz
author_facet von Stosch, Moritz
de Azevedo, Cristiana Rodrigues
Luís, Mauro
de Azevedo, Sebastiao Feyo
Oliveira, Rui
author_role author
author2 de Azevedo, Cristiana Rodrigues
Luís, Mauro
de Azevedo, Sebastiao Feyo
Oliveira, Rui
author2_role author
author
author
author
dc.contributor.none.fl_str_mv DQ - Departamento de Química
LAQV@REQUIMTE
RUN
dc.contributor.author.fl_str_mv von Stosch, Moritz
de Azevedo, Cristiana Rodrigues
Luís, Mauro
de Azevedo, Sebastiao Feyo
Oliveira, Rui
dc.subject.por.fl_str_mv Elementary flux modes
Flux data analysis
Fluxome data analysis
Principal component analysis
Principle elementary modes
Structural Biology
Biochemistry
Molecular Biology
Computer Science Applications
Applied Mathematics
topic Elementary flux modes
Flux data analysis
Fluxome data analysis
Principal component analysis
Principle elementary modes
Structural Biology
Biochemistry
Molecular Biology
Computer Science Applications
Applied Mathematics
description Deutscher Akademischer Austausch Dienst, Reference number: 6818.
publishDate 2016
dc.date.none.fl_str_mv 2016
2016-01-01T00:00:00Z
2023-06-16T22:17:03Z
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.uri.fl_str_mv http://hdl.handle.net/10362/154050
url http://hdl.handle.net/10362/154050
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 1471-2105
PURE: 14322148
https://doi.org/10.1186/s12859-016-1063-0
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv 19
application/pdf
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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