fREDUCE: Detection of degenerate regulatory elements using correlation with expression. Results: 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. Conclusion: 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
References in zbMATH (referenced in 2 articles )
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- Comin, Matteo; Verzotto, Davide: Filtering degenerate patterns with application to protein sequence analysis (2013)
- Wu, Randy Z.; Chaivorapol, Christina; Zheng, Jiashun; Li, Hao; Liang, Shoudan: Freduce: Detection of degenerate regulatory elements using correlation with expression (2007) ioport