fREDUCE: Detection of degenerate regulatory elements using correlation with expression

Background: 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. 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 accur...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Randy Z. Wu, Christina Chaivorapol, Jiashun Zheng, Hao Li, Shoudan Liang
• Keywords: Binding Sites, BMCBI 2007, Transcription Factor, Transcriptional Regulation