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Transcription Factor Map Alignment of Promoter Regions
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, thu...
Autores principales: | , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2006
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1464811/ https://www.ncbi.nlm.nih.gov/pubmed/16733547 http://dx.doi.org/10.1371/journal.pcbi.0020049 |
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author | Blanco, Enrique Messeguer, Xavier Smith, Temple F Guigó, Roderic |
author_facet | Blanco, Enrique Messeguer, Xavier Smith, Temple F Guigó, Roderic |
author_sort | Blanco, Enrique |
collection | PubMed |
description | 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. |
format | Text |
id | pubmed-1464811 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2006 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-14648112006-05-26 Transcription Factor Map Alignment of Promoter Regions Blanco, Enrique Messeguer, Xavier Smith, Temple F Guigó, Roderic PLoS Comput Biol Research Article 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. Public Library of Science 2006-05 2006-05-26 /pmc/articles/PMC1464811/ /pubmed/16733547 http://dx.doi.org/10.1371/journal.pcbi.0020049 Text en © 2006 Blanco et al. http://creativecommons.org/licenses/by/4.0/ 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 properly credited. |
spellingShingle | Research Article Blanco, Enrique Messeguer, Xavier Smith, Temple F Guigó, Roderic Transcription Factor Map Alignment of Promoter Regions |
title | Transcription Factor Map Alignment of Promoter Regions |
title_full | Transcription Factor Map Alignment of Promoter Regions |
title_fullStr | Transcription Factor Map Alignment of Promoter Regions |
title_full_unstemmed | Transcription Factor Map Alignment of Promoter Regions |
title_short | Transcription Factor Map Alignment of Promoter Regions |
title_sort | transcription factor map alignment of promoter regions |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1464811/ https://www.ncbi.nlm.nih.gov/pubmed/16733547 http://dx.doi.org/10.1371/journal.pcbi.0020049 |
work_keys_str_mv | AT blancoenrique transcriptionfactormapalignmentofpromoterregions AT messeguerxavier transcriptionfactormapalignmentofpromoterregions AT smithtemplef transcriptionfactormapalignmentofpromoterregions AT guigoroderic transcriptionfactormapalignmentofpromoterregions |