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Title: Transcription factor map alignment of promoter regions
Author: Blanco García, Enrique
Messeguer Peypoch, Xavier
Smith, T. F.
Guigó Serra, Roderic
Keywords: Genoma humà
Expressió gènica
Transcripció genètica
Human genome
Gene expression
Genetic transcription
Issue Date: May-2006
Publisher: Public Library of Science (PLoS)
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.
Note: Reproducció del document publicat a:
It is part of: PLoS Computational Biology, 2006, vol. 2, num. 5, p. e49
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ISSN: 1553-734X
Appears in Collections:Articles publicats en revistes (Genètica, Microbiologia i Estadística)

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