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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 co-regulated genes, which can be derived from the microarray clustering analysis.

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