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rdf:type |
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lifeskim:mentions |
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pubmed:issue |
3
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pubmed:dateCreated |
2001-2-22
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pubmed:abstractText |
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/.
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pubmed:grant |
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pubmed:commentsCorrections |
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-10068691,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-10390542,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-10592181,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-10592182,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-10592242,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-10637320,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-10734204,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-10854408,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-1569108,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-1574589,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-1731067,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-2172928,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-2184437,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-2919167,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-7584402,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-8211139,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-8520488,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-9254694,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-9278503,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-9466250,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-9682052,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-9767562,
http://linkedlifedata.com/resource/pubmed/commentcorrection/11160901-9813115
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pubmed:language |
eng
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pubmed:journal |
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pubmed:citationSubset |
IM
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pubmed:chemical |
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pubmed:status |
MEDLINE
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pubmed:month |
Feb
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pubmed:issn |
1362-4962
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pubmed:author |
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pubmed:issnType |
Electronic
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pubmed:day |
1
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pubmed:volume |
29
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pubmed:owner |
NLM
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pubmed:authorsComplete |
Y
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pubmed:pagination |
774-82
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pubmed:dateRevised |
2009-11-18
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pubmed:meshHeading |
pubmed-meshheading:11160901-Base Sequence,
pubmed-meshheading:11160901-Binding Sites,
pubmed-meshheading:11160901-DNA, Bacterial,
pubmed-meshheading:11160901-Databases, Factual,
pubmed-meshheading:11160901-Escherichia coli,
pubmed-meshheading:11160901-Gammaproteobacteria,
pubmed-meshheading:11160901-Genes, Bacterial,
pubmed-meshheading:11160901-Genome, Bacterial,
pubmed-meshheading:11160901-Phylogeny,
pubmed-meshheading:11160901-Protein Binding,
pubmed-meshheading:11160901-Sequence Alignment,
pubmed-meshheading:11160901-Sequence Homology, Nucleic Acid,
pubmed-meshheading:11160901-Transcription Factors
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pubmed:year |
2001
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pubmed:articleTitle |
Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes.
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pubmed:affiliation |
The Wadsworth Center for Laboratories and Research, New York State Department of Health, Albany, NY 12201, USA.
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pubmed:publicationType |
Journal Article,
Research Support, U.S. Gov't, P.H.S.
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