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Published online before print August 16, 2001, 10.1101/gr.158301
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Vol. 11, Issue 9, 1567-1573, September 2001

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

Kenneth Birnbaum,1,3 Philip N. Benfey,1,3 and Dennis E. Shasha2,3,4

1 Department of Biology, New York University, New York, New York 10003, USA; 2 Courant Institute of Mathematical Sciences, New York University, New York, New York 10012, USA

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 from Saccharomyces cerevisiae.

3 All authors contributed equally to this work.

4 Corresponding author.

11:1567-1573 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
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