Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs

Abstract

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. © 2006 Mao and Zheng; licensee BioMed Central Ltd.