Thu, 21 Aug 2008 17:23:27 BST CiteULike: oscarluoinau library [3 articles] http://www.citeulike.org/user/oscarluoinau CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/oscarluoinau/article/1249314 <i>BMC Bioinformatics, Vol. 8 (24 April 2007), 138.</i> Multiple Non-Collinear TF-map Alignments of Promoter Regions Enrique Blanco Roderic Guigo Xavier Messeguer doi:10.1186/1471-2105-8-138 BMC Bioinformatics, Vol. 8 (24 April 2007), 138. 2007-04-25T04:35:01-00:00 2007 BMC Bioinformatics 1471-2105 8 138 project http://www.citeulike.org/user/oscarluoinau/article/671638 <i>PLoS Computational Biology, Vol. 2, No. 5. (1 May 2006), e49.</i><br /><br />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. Transcription Factor Map Alignment of Promoter Regions Enrique Blanco Xavier Messeguer Temple Smith Roderic Guigó doi:10.1371/journal.pcbi.0020049 PLoS Computational Biology, Vol. 2, No. 5. (1 May 2006), e49. 2006-05-26T18:52:47-00:00 2006 PLoS Computational Biology 2 5 e49 project http://www.citeulike.org/user/oscarluoinau/article/106364 <i>Nature, Vol. aop, No. current. (27 February 2005), pp. 338-345.</i> Systematic discovery of regulatory motifs in human promoters and 3[prime] UTRs by comparison of several mammals Xiaohui Xie Jun Lu EJ Kulbokas Todd Golub Vamsi Mootha Kerstin Lindblad-Toh Eric Lander Manolis Kellis doi:10.1038/nature03441 Nature, Vol. aop, No. current. (27 February 2005), pp. 338-345. 2005-02-28T05:59:22-00:00 2005 Nature 0028-0836 aop current 338 345 Nature Publishing Group project