Please use this identifier to cite or link to this item:
http://hdl.handle.net/2445/43418
Full metadata record
DC Field | Value | Language |
---|---|---|
dc.contributor.author | Blanco García, Enrique | - |
dc.contributor.author | Messeguer Peypoch, Xavier | - |
dc.contributor.author | Smith, T. F. | - |
dc.contributor.author | Guigó Serra, Roderic | - |
dc.date.accessioned | 2013-05-14T15:28:20Z | - |
dc.date.available | 2013-05-14T15:28:20Z | - |
dc.date.issued | 2006-05 | - |
dc.identifier.issn | 1553-734X | - |
dc.identifier.uri | http://hdl.handle.net/2445/43418 | - |
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. | - |
dc.format.extent | 14 p. | - |
dc.format.mimetype | application/pdf | - |
dc.language.iso | eng | - |
dc.publisher | Public Library of Science (PLoS) | - |
dc.relation.isformatof | Reproducció del document publicat a: http://dx.doi.org/10.1371/journal.pcbi.0020049 | - |
dc.relation.ispartof | PLoS Computational Biology, 2006, vol. 2, num. 5, p. e49 | - |
dc.relation.uri | http://dx.doi.org/10.1371/journal.pcbi.0020049 | - |
dc.rights | cc-by (c) Blanco García, Enrique et al., 2006 | - |
dc.rights.uri | http://creativecommons.org/licenses/by/3.0/es | - |
dc.source | Articles publicats en revistes (Genètica, Microbiologia i Estadística) | - |
dc.subject.classification | Genoma humà | - |
dc.subject.classification | Expressió gènica | - |
dc.subject.classification | Transcripció genètica | - |
dc.subject.other | Human genome | - |
dc.subject.other | Gene expression | - |
dc.subject.other | Genetic transcription | - |
dc.title | Transcription factor map alignment of promoter regions | eng |
dc.type | info:eu-repo/semantics/article | - |
dc.type | info:eu-repo/semantics/publishedVersion | - |
dc.identifier.idgrec | 600243 | - |
dc.date.updated | 2013-05-14T15:28:20Z | - |
dc.rights.accessRights | info:eu-repo/semantics/openAccess | - |
dc.identifier.pmid | 16733547 | - |
Appears in Collections: | Articles publicats en revistes (Genètica, Microbiologia i Estadística) |
Files in This Item:
File | Description | Size | Format | |
---|---|---|---|---|
600243.pdf | 439.09 kB | Adobe PDF | View/Open |
This item is licensed under a Creative Commons License