A principal components method constrained by elementary flux modes
Autor(a) principal: | |
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Data de Publicação: | 2016 |
Outros Autores: | , , , |
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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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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7160 |
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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 |
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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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1799138142126604288 |