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  • Title: Combining comparative genomics with de novo motif discovery to identify human transcription factor DNA-binding motifs.
    Author: Mao L, Zheng WJ.
    Journal: BMC Bioinformatics; 2006 Dec 12; 7 Suppl 4(Suppl 4):S21. PubMed ID: 17217514.
    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 co-regulated genes, which can be derived from the microarray clustering analysis.
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