Multiple non-collinear TF-map alignments of promoter regions

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Blanco E, Guigó R, Messeguer X. Multiple non-collinear TF-map alignments of promoter regions. BMC Bioinformatics. 2007; 8: 138. DOI 10.1186/1471-2105-8-138
http://hdl.handle.net/10230/12926
To cite or link this document: http://hdl.handle.net/10230/12926
dc.contributor.author Blanco, Enrique
dc.contributor.author Guigó Serra, Roderic
dc.contributor.author Messeguer, Xavier
dc.contributor.other Universitat Pompeu Fabra
dc.date.accessioned 2011-10-26T11:07:52Z
dc.date.available 2011-10-26T11:07:52Z
dc.date.issued 2007
dc.identifier.citation Blanco E, Guigó R, Messeguer X. Multiple non-collinear TF-map alignments of promoter regions. BMC Bioinformatics. 2007; 8: 138. DOI 10.1186/1471-2105-8-138
dc.identifier.issn 1471-2105
dc.identifier.uri http://hdl.handle.net/10230/12926
dc.description.abstract Background: The analysis of the promoter sequence of genes with similar expression patterns is a basic tool to annotate common regulatory elements. Multiple sequence alignments are on the basis of most comparative approaches. The characterization of regulatory regions from coexpressed genes at the sequence level, however, does not yield satisfactory results in many occasions as promoter regions of genes sharing similar expression programs often do not show nucleotide sequence conservation. Results: In a recent approach to circumvent this limitation, we proposed to align the maps of predicted transcription factors (referred as TF-maps) instead of the nucleotide sequence of two related promoters, taking into account the label of the corresponding factor and the position in the primary sequence. We have now extended the basic algorithm to permit multiple promoter comparisons using the progressive alignment paradigm. In addition, non-collinear conservation blocks might now be identified in the resulting alignments. We have optimized the parameters of the algorithm in a small, but well-characterized collection of human-mouse-chicken-zebrafish orthologous gene promoters. Conclusion: Results in this dataset indicate that TF-map alignments are able to detect high-level regulatory conservation at the promoter and the 3'UTR gene regions, which cannot be detected by the typical sequence alignments. Three particular examples are introduced here to illustrate the power of the multiple TF-map alignments to characterize conserved regulatory elements in absence of sequence similarity. We consider this kind of approach can be extremely useful in the future to annotate potential transcription factor binding sites on sets of co-regulated genes from high-throughput expression experiments.
dc.language.iso eng
dc.publisher BioMed Central
dc.rights © 2007 Blanco et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. This article is also available from: http://www.biomedcentral.com/1471-2105/8/138
dc.rights.uri http://creativecommons.org/licenses/by/2.0/
dc.subject.other Factors de transcripció
dc.subject.other Genètica -- Tècnica
dc.title Multiple non-collinear TF-map alignments of promoter regions
dc.type info:eu-repo/semantics/article
dc.identifier.doi http://dx.doi.org/10.1186/1471-2105-8-138
dc.subject.keyword Promoter regions
dc.subject.keyword Nucleotide sequence
dc.subject.keyword TF-map alignment
dc.subject.keyword Non-collinear conservation blocks
dc.subject.keyword 3'UTR
dc.rights.accessRights info:eu-repo/semantics/openAccess
dc.type.version info:eu-repo/semantics/publishedVersion


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