McCue, L. A.Thompson, WilliamCarmack, C. StevenRyan, Michael P.Liu, JunDerbyshire, VictoriaLawrence, Charles E.2016-05-162001McCue, L. A. 2001. “Phylogenetic Footprinting of Transcription Factor Binding Sites in Proteobacterial Genomes.” Nucleic Acids Research 29 (3) (February 1): 774–782. doi:10.1093/nar/29.3.774. http://dx.doi.org/10.1093/nar/29.3.774.1362-4962http://nrs.harvard.edu/urn-3:HUL.InstRepos:27002732Toward 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/.en-USJournal Article2016-05-1610.1093/nar/29.3.774