Combining Comparative Genomics with de novo Motif Discovery to Identify Human Transcription Factor DNA-Binding Motifs

Background: As more and more genomes are sequenced, comparative genomics approaches provide a methodology for identifying conserved regulatory elements that may be involved in gene regulations. Results: We developed a novel method to combine comparative genomics with de novo motif discovery to identify human transcription factor binding motifs that are overrepresented and conserved in the upstream regions of a set of co-regulated genes. The method is validated by analyzing a well-characterized muscle specific gene set, and the results showed that our approach performed better than the existing programs in terms of sensitivity and prediction rate. Conclusion: The newly developed method can be used to extract regulatory signals in coregulated genes, which can be derived from the microarray clustering analysis. Background Transcription factors (TFs) regulate the expression of genes by interacting with cis-regulatory elements in DNA sequences in response to internal and external stimuli. ...

• Type: Conference
• Year: 2006
• Where: IMSCCS
• Authors: Linyong Mao, W. Jim Zheng
• Keywords: Co-regulated Genes, Comparative Genomics, IMSCCS 2006, Novo Motif Discovery