Identifying tissue-selective transcription factor binding sites in vertebrate promoters

Smith, A. D., Sumazin, P., Zhang, M. Q. (February 2005) Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc Natl Acad Sci U S A, 102 (5). pp. 1560-5. ISSN 0027-8424 (Print)

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DOI: 10.1073/pnas.0406123102


We present a computational method aimed at systematically identifying tissue-selective transcription factor binding sites. Our method focuses on the differences between sets of promoters that are associated with differentially expressed genes, and it is effective at identifying the highly degenerate motifs that characterize vertebrate transcription factor binding sites. Results on simulated data indicate that our method detects motifs with greater accuracy than the leading methods, and its detection of strongly overrepresented motifs is nearly perfect. We present motifs identified by our method as the most overrepresented in promoters of liver- and muscle-selective genes, demonstrating that our method accurately identifies known transcription factor binding sites and previously uncharacterized motifs.

Item Type: Paper
Uncontrolled Keywords: Animals Base Sequence Binding Sites Likelihood Functions Liver metabolism Models Genetic Promoter Regions Reproducibility of Results Transcription Factors genetics metabolism Vertebrates genetics
Subjects: Investigative techniques and equipment
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: CSHL Librarian
Date: 1 February 2005
Date Deposited: 06 Jan 2012 14:13
Last Modified: 09 Nov 2017 16:49
PMCID: PMC547828
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