cis Element/Transcription Factor Analysis (cis/TF): A Method for Discovering Transcription Factor/cis Element Relationships

  1. Kenneth Birnbaum1,3,
  2. Philip N. Benfey1,3, and
  3. Dennis E. Shasha2,3,4
  1. 1Department of Biology, New York University, New York, New York 10003, USA; 2Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA

Abstract

We report a simple new algorithm, cis/TF, that uses genomewide expression data and the full genomic sequence to match transcription factors to their binding sites. Most previous computational methods discovered binding sites by clustering genes having similar expression patterns and then identifying over-represented subsequences in the promoter regions of those genes. By contrast, cis/TF asserts that B is a likely binding site of a transcription factor T if the expression pattern of T is correlated to the composite expression patterns of all genes containing B, even when those genes are not mutually correlated. Thus, our method focuses on binding sites rather than genes. The algorithm has successfully identified experimentally-supported transcription factor binding relationships in tests on several data sets fromSaccharomyces cerevisiae.

Footnotes

  • ↵3 All authors contributed equally to this work.

  • ↵4 Corresponding author.

  • E-MAIL shasha{at}cs.nyu.edu; FAX (212) 995-4204.

  • Article published on-line before print: Genome Res.,10.1101/gr.158301.

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.158301.

    • Received February 27, 2001.
    • Accepted June 13, 2001.
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  1. Published in Advance August 16, 2001, doi: 10.1101/gr.158301 Genome Res. 11: 1567-1573 Cold Spring Harbor Laboratory Press

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