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. 2005 Oct 27:6:262.
doi: 10.1186/1471-2105-6-262.

Using hexamers to predict cis-regulatory motifs in Drosophila

Bob Y Chan  1 , Dennis Kibler
Affiliations

Using hexamers to predict cis-regulatory motifs in Drosophila

Bob Y Chan et al. BMC Bioinformatics. .

Abstract

Background: Cis-regulatory modules (CRMs) are short stretches of DNA that help regulate gene expression in higher eukaryotes. They have been found up to 1 megabase away from the genes they regulate and can be located upstream, downstream, and even within their target genes. Due to the difficulty of finding CRMs using biological and computational techniques, even well-studied regulatory systems may contain CRMs that have not yet been discovered.

Results: We present a simple, efficient method (HexDiff) based only on hexamer frequencies of known CRMs and non-CRM sequence to predict novel CRMs in regulatory systems. On a data set of 16 gap and pair-rule genes containing 52 known CRMs, predictions made by HexDiff had a higher correlation with the known CRMs than several existing CRM prediction algorithms: Ahab, Cluster Buster, MSCAN, MCAST, and LWF. After combining the results of the different algorithms, 10 putative CRMs were identified and are strong candidates for future study. The hexamers used by HexDiff to distinguish between CRMs and non-CRM sequence were also analyzed and were shown to be enriched in regulatory elements.

Conclusion: HexDiff provides an efficient and effective means for finding new CRMs based on known CRMs, rather than known binding sites.

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References

    1. Davidson EH, McClay DR, Hood L. Regulatory gene networks and the properties of the developmental process. Proc Natl Acad Sci U S A. 2003;100:1475–1480. doi: 10.1073/pnas.0437746100. - DOI - PMC - PubMed
    1. Qiu P. Recent advances in computational promoter analysis in understanding the transcriptional regulatory network. Biochem Biophys Res Commun. 2003;309:495–501. doi: 10.1016/j.bbrc.2003.08.052. - DOI - PubMed
    1. Laimins LA, Gruss P, Pozzatti R, Khoury G. Characterization of enhancer elements in the long terminal repeat of Moloney murine sarcoma virus. J Virol. 1984;49:183–189. - PMC - PubMed
    1. Qin Y, Kong LK, Poirier C, Truong C, Overbeek PA, Bishop CE. Long-range activation of Sox9 in Odd Sex (Ods) mice. Hum Mol Genet. 2004;13:1213–1218. doi: 10.1093/hmg/ddh141. - DOI - PubMed
    1. Wasserman WW, Fickett JW. Identification of regulatory regions which confer muscle-specific gene expression. J Mol Biol. 1998;278:167–181. doi: 10.1006/jmbi.1998.1700. - DOI - PubMed

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