Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Export

@article{citeulike:876627, abstract = {Toward the goal of identifying complete sets of transcription factor (TF)-binding sites in the genomes of several gamma proteobacteria, and hence describing their transcription regulatory networks, we present a phylogenetic footprinting method for identifying these sites. Probable transcription regulatory sites upstream of Escherichia coli genes were identified by cross-species comparison using an extended Gibbs sampling algorithm. Close examination of a study set of 184 genes with documented transcription regulatory sites revealed that when orthologous data were available from at least two other gamma proteobacterial species, 81\% of our predictions corresponded with the documented sites, and 67\% corresponded when data from only one other species were available. That the remaining predictions included bona fide TF-binding sites was proven by affinity purification of a putative transcription factor (YijC) bound to such a site upstream of the fabA gene. Predicted regulatory sites for 2097 E.coli genes are available at http://www.wadsworth.org/resnres/bioinfo/.}, address = {The Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany, NY 12201, USA.}, author = {McCue, L. and Thompson, W. and Carmack, C. and Ryan, M. P. and Liu, J. S. and Derbyshire, V. and Lawrence, C. E.}, citeulike-article-id = {876627}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/nar/29.3.774}, citeulike-linkout-1 = {http://nar.oxfordjournals.org/cgi/content/abstract/29/3/774}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/11160901}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=11160901}, day = {1}, doi = {10.1093/nar/29.3.774}, issn = {1362-4962}, journal = {Nucleic Acids Res}, keywords = {bacteria, footprinting, motif, phylogeny, prokaryote, regulation, tfbs}, month = {February}, number = {3}, pages = {774--782}, posted-at = {2008-08-07 16:23:07}, priority = {2}, title = {Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes.}, url = {http://dx.doi.org/10.1093/nar/29.3.774}, volume = {29}, year = {2001} }

TY - JOUR ID - citeulike:876627 L3 - citeulike-article-id:876627 N2 - Toward the goal of identifying complete sets of transcription factor (TF)-binding sites in the genomes of several gamma proteobacteria, and hence describing their transcription regulatory networks, we present a phylogenetic footprinting method for identifying these sites. Probable transcription regulatory sites upstream of Escherichia coli genes were identified by cross-species comparison using an extended Gibbs sampling algorithm. Close examination of a study set of 184 genes with documented transcription regulatory sites revealed that when orthologous data were available from at least two other gamma proteobacterial species, 81% of our predictions corresponded with the documented sites, and 67% corresponded when data from only one other species were available. That the remaining predictions included bona fide TF-binding sites was proven by affinity purification of a putative transcription factor (YijC) bound to such a site upstream of the fabA gene. Predicted regulatory sites for 2097 E.coli genes are available at http://www.wadsworth.org/resnres/bioinfo/. IS - 3 JF - Nucleic Acids Res SN - 1362-4962 AD - The Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany, NY 12201, USA. EP - 782 TI - Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. VL - 29 SP - 774 KW - bacteria KW - footprinting KW - motif KW - phylogeny KW - prokaryote KW - regulation KW - tfbs AU - McCue, L AU - Thompson, W AU - Carmack, C AU - Ryan, MP AU - Liu, JS AU - Derbyshire, V AU - Lawrence, CE PY - 2001/02/01/ UR - http://dx.doi.org/10.1093/nar/29.3.774 ER -