Transcription factor map alignment of promoter regions
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- dc.contributor.author Blanco, Enriqueca
- dc.contributor.author Messeguer, Xavierca
- dc.contributor.author Smith, Temple F.ca
- dc.contributor.author Guigó Serra, Rodericca
- dc.date.accessioned 2011-11-28T11:08:18Z
- dc.date.available 2011-11-28T11:08:18Z
- dc.date.issued 2006ca
- dc.description.abstract We address the problem of comparing and characterizing the promoter regions of genes with similar expression patterns. This remains a challenging problem in sequence analysis, because often the promoter regions of co-expressed genes do not show discernible sequence conservation. In our approach, thus, we have not directly compared the nucleotide sequence of promoters. Instead, we have obtained predictions of transcription factor binding sites, annotated the predicted sites with the labels of the corresponding binding factors, and aligned the resulting sequences of labels—to which we refer here as transcription factor maps (TF-maps). To obtain the global pairwise alignment of two TF-maps, we have adapted an algorithm initially developed to align restriction enzyme maps. We have optimized the parameters of the algorithm in a small, but well-curated, collection of human–mouse orthologous gene pairs. Results in this dataset, as well as in an independent much larger dataset from the CISRED database, indicate that TF-map alignments are able to uncover conserved regulatory elements, which cannot be detected by the typical sequence alignments.en
- dc.description.sponsorship This work was supported by grant BIO2003–05073 from/nthe Spanish Ministerio de Ciencia y Tecnología and Instituto/nNacional de Bioinformática to RG.en
- dc.format.mimetype application/pdfca
- dc.identifier.citation Blanco E, Messeguer X, Smith T F, Guigó R. Transcription factor map alignment of promoter regions. PLoS Comput. Biol. 2006; 2(5):e49. DOI 10.1371/journal.pcbi.0020049
- dc.identifier.doi http://dx.doi.org/10.1371/journal.pcbi.0020049
- dc.identifier.issn 1553-734X
- dc.identifier.uri http://hdl.handle.net/10230/13156
- dc.language.iso engca
- dc.publisher Public Library of Science (PLoS)ca
- dc.relation.ispartof PLOS Computational Biology. 2006;2(5):e49
- dc.relation.projectID info:eu-repo/grantAgreement/ES/2PN/BIO2003–05073
- dc.rights © 2006 Blanco et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.5/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.ca
- dc.rights.accessRights info:eu-repo/semantics/openAccessen
- dc.rights.uri http://creativecommons.org/licenses/by/2.5/
- dc.subject.keyword Species specificityen
- dc.subject.keyword Algorithmsen
- dc.subject.keyword Animalsen
- dc.subject.keyword Humansen
- dc.subject.keyword Miceen
- dc.subject.keyword Chromosome mappingen
- dc.subject.keyword Promoter regionsen
- dc.subject.keyword Restriction mapping methoden
- dc.subject.keyword Transcription factorsen
- dc.subject.other Biologia molecularca
- dc.subject.other Biologia computacional -- Mètodesca
- dc.subject.other Genòmica -- Models estadísticsca
- dc.subject.other Genètica -- Tècnicaca
- dc.subject.other Factors de transcripcióca
- dc.title Transcription factor map alignment of promoter regionsca
- dc.type info:eu-repo/semantics/articleca
- dc.type.version info:eu-repo/semantics/publishedVersionen