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Using hexamers to predict cis-regulatory motifs in Drosophila

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...

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Detalles Bibliográficos
Autores principales: Chan, Bob Y, Kibler, Dennis
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1291357/
https://www.ncbi.nlm.nih.gov/pubmed/16253142
http://dx.doi.org/10.1186/1471-2105-6-262
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author Chan, Bob Y
Kibler, Dennis
author_facet Chan, Bob Y
Kibler, Dennis
author_sort Chan, Bob Y
collection PubMed
description 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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spelling pubmed-12913572005-12-06 Using hexamers to predict cis-regulatory motifs in Drosophila Chan, Bob Y Kibler, Dennis BMC Bioinformatics Methodology Article 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. BioMed Central 2005-10-27 /pmc/articles/PMC1291357/ /pubmed/16253142 http://dx.doi.org/10.1186/1471-2105-6-262 Text en Copyright © 2005 Chan and Kibler; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Methodology Article
Chan, Bob Y
Kibler, Dennis
Using hexamers to predict cis-regulatory motifs in Drosophila
title Using hexamers to predict cis-regulatory motifs in Drosophila
title_full Using hexamers to predict cis-regulatory motifs in Drosophila
title_fullStr Using hexamers to predict cis-regulatory motifs in Drosophila
title_full_unstemmed Using hexamers to predict cis-regulatory motifs in Drosophila
title_short Using hexamers to predict cis-regulatory motifs in Drosophila
title_sort using hexamers to predict cis-regulatory motifs in drosophila
topic Methodology Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1291357/
https://www.ncbi.nlm.nih.gov/pubmed/16253142
http://dx.doi.org/10.1186/1471-2105-6-262
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