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Transcription factor map alignment of promoter regions
Blanco, Enrique; Messeguer, Xavier; Smith, Temple F.; Guigó Serra, Roderic
Universitat Pompeu Fabra
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.
This work was supported by grant BIO2003–05073 fromthe Spanish Ministerio de Ciencia y Tecnología and InstitutoNacional de Bioinformática to RG.
Biologia molecular
Biologia computacional -- Mètodes
Genòmica -- Models estadístics
Genètica -- Tècnica
Factors de transcripció
Species specificity
Chromosome mapping
Promoter regions
Restriction mapping method
Transcription factors
(c) 2006 Blanco et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Public Library of Science (PLoS)

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