Topological comparison of methods for predicting transcriptional cooperativity in yeast

Background: The cooperative interaction between transcription factors has a decisive role in the control of the fate of the eukaryotic cell. Computational approaches for characterizing cooperative transcription factors in yeast, however, are based on different rationales and provide a low overlap be...

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Detalles Bibliográficos
Autores: Aguilar, Daniel, Oliva Miguel, Baldomero
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2008
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10230/16430
Acceso en línea:http://hdl.handle.net/10230/16430
http://dx.doi.org/10.1186/1471-2164-9-137
Access Level:acceso abierto
Palabra clave:Transcripció genètica -- Regulació
Cèl·lules eucariotes -- Aspectes genètics
Interaccions proteïna-proteïna
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spelling Topological comparison of methods for predicting transcriptional cooperativity in yeastAguilar, DanielOliva Miguel, BaldomeroTranscripció genètica -- RegulacióCèl·lules eucariotes -- Aspectes genèticsInteraccions proteïna-proteïnaBackground: The cooperative interaction between transcription factors has a decisive role in the control of the fate of the eukaryotic cell. Computational approaches for characterizing cooperative transcription factors in yeast, however, are based on different rationales and provide a low overlap between their results. Because the wealth of information contained in protein interaction networks and regulatory networks has proven highly effective in elucidating functional relationships between proteins, we compared different sets of cooperative transcription factor pairs (predicted by four different computational methods) within the frame of those networks. Results: /nOur results show that the overlap between the sets of cooperative transcription factors predicted by the different methods is low yet significant. Cooperative transcription factors predicted by all methods are closer and more clustered in the protein interaction network than expected by chance. On the other hand, members of a cooperative transcription factor pair neither seemed to regulate each other nor shared similar regulatory inputs, although they do regulate similar groups of target genes. Conclusion: Despite the different definitions of transcriptional cooperativity and the different computational approaches used to characterize cooperativity between transcription factors, the analysis of their roles in the framework of the protein interaction network and the regulatory network indicates a common denominator for the predictions under study. The knowledge of the shared topological properties of cooperative transcription factor pairs in both networks can be useful not only for designing better prediction methods but also for better understanding the complexities of transcriptional control in eukaryotes.This work has been supported by grants from the Spanish Ministerio de Educación y Ciencia (MEC, BIO02005-00533, PROFIT PSE-010000-2007-1 and FIT-350300-2006-40/41/42), INFOBIOMED-NoE (IST-507585) and ANEURIST. DA acknowledges the financial support of the Juan de la Cierva program (IST-507585) of the MEC.BioMed Central201220122008info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionapplication/pdfapplication/pdfhttp://hdl.handle.net/10230/16430http://dx.doi.org/10.1186/1471-2164-9-137reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésBMC Genomics. 2008;9:137© 2008 Aguilar et al. Creative Commons Attribution Licensehttp://creativecommons.org/licenses/by/2.0/info:eu-repo/semantics/openAccessoai:recercat.cat:10230/164302026-05-29T05:05:01Z
dc.title.none.fl_str_mv Topological comparison of methods for predicting transcriptional cooperativity in yeast
title Topological comparison of methods for predicting transcriptional cooperativity in yeast
spellingShingle Topological comparison of methods for predicting transcriptional cooperativity in yeast
Aguilar, Daniel
Transcripció genètica -- Regulació
Cèl·lules eucariotes -- Aspectes genètics
Interaccions proteïna-proteïna
title_short Topological comparison of methods for predicting transcriptional cooperativity in yeast
title_full Topological comparison of methods for predicting transcriptional cooperativity in yeast
title_fullStr Topological comparison of methods for predicting transcriptional cooperativity in yeast
title_full_unstemmed Topological comparison of methods for predicting transcriptional cooperativity in yeast
title_sort Topological comparison of methods for predicting transcriptional cooperativity in yeast
dc.creator.none.fl_str_mv Aguilar, Daniel
Oliva Miguel, Baldomero
author Aguilar, Daniel
author_facet Aguilar, Daniel
Oliva Miguel, Baldomero
author_role author
author2 Oliva Miguel, Baldomero
author2_role author
dc.subject.none.fl_str_mv Transcripció genètica -- Regulació
Cèl·lules eucariotes -- Aspectes genètics
Interaccions proteïna-proteïna
topic Transcripció genètica -- Regulació
Cèl·lules eucariotes -- Aspectes genètics
Interaccions proteïna-proteïna
description Background: The cooperative interaction between transcription factors has a decisive role in the control of the fate of the eukaryotic cell. Computational approaches for characterizing cooperative transcription factors in yeast, however, are based on different rationales and provide a low overlap between their results. Because the wealth of information contained in protein interaction networks and regulatory networks has proven highly effective in elucidating functional relationships between proteins, we compared different sets of cooperative transcription factor pairs (predicted by four different computational methods) within the frame of those networks. Results: /nOur results show that the overlap between the sets of cooperative transcription factors predicted by the different methods is low yet significant. Cooperative transcription factors predicted by all methods are closer and more clustered in the protein interaction network than expected by chance. On the other hand, members of a cooperative transcription factor pair neither seemed to regulate each other nor shared similar regulatory inputs, although they do regulate similar groups of target genes. Conclusion: Despite the different definitions of transcriptional cooperativity and the different computational approaches used to characterize cooperativity between transcription factors, the analysis of their roles in the framework of the protein interaction network and the regulatory network indicates a common denominator for the predictions under study. The knowledge of the shared topological properties of cooperative transcription factor pairs in both networks can be useful not only for designing better prediction methods but also for better understanding the complexities of transcriptional control in eukaryotes.
publishDate 2008
dc.date.none.fl_str_mv 2008
2012
2012
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10230/16430
http://dx.doi.org/10.1186/1471-2164-9-137
url http://hdl.handle.net/10230/16430
http://dx.doi.org/10.1186/1471-2164-9-137
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv BMC Genomics. 2008;9:137
dc.rights.none.fl_str_mv © 2008 Aguilar et al. Creative Commons Attribution License
http://creativecommons.org/licenses/by/2.0/
info:eu-repo/semantics/openAccess
rights_invalid_str_mv © 2008 Aguilar et al. Creative Commons Attribution License
http://creativecommons.org/licenses/by/2.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv BioMed Central
publisher.none.fl_str_mv BioMed Central
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
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