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Open Access Methodology article

fREDUCE: Detection of degenerate regulatory elements using correlation with expression

Randy Z Wu1, Christina Chaivorapol1, Jiashun Zheng1, Hao Li1* and Shoudan Liang2*

Author Affiliations

1 Department of Biochemistry and Biophysics, UCSF. 1700 4th Street, San Francisco, CA 94143-2542, USA

2 Department of Bioinformatics and Computational Biology, The University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Blvd, Unit 237, Houston, TX 77030-4009, USA

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BMC Bioinformatics 2007, 8:399  doi:10.1186/1471-2105-8-399

Published: 17 October 2007



The precision of transcriptional regulation is made possible by the specificity of physical interactions between transcription factors and their cognate binding sites on DNA. A major challenge is to decipher transcription factor binding sites from sequence and functional genomic data using computational means. While current methods can detect strong binding sites, they are less sensitive to degenerate motifs.


We present fREDUCE, a computational method specialized for the detection of weak or degenerate binding motifs from gene expression or ChIP-chip data. fREDUCE is built upon the widely applied program REDUCE, which elicits motifs by global statistical correlation of motif counts with expression data. fREDUCE introduces several algorithmic refinements that allow efficient exhaustive searches of oligonucleotides with a specified number of degenerate IUPAC symbols. On yeast ChIP-chip benchmarks, fREDUCE correctly identified motifs and their degeneracies with accuracies greater than its predecessor REDUCE as well as other known motif-finding programs. We have also used fREDUCE to make novel motif predictions for transcription factors with poorly characterized binding sites.


We demonstrate that fREDUCE is a valuable tool for the prediction of degenerate transcription factor binding sites, especially from array datasets with weak signals that may elude other motif detection methods.