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Article: Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation

TitlePosition and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation
Authors
Issue Date2007
PublisherOxford University Press. The Journal's web site is located at http://nar.oxfordjournals.org/
Citation
Nucleic Acids Research, 2007, v. 35 n. 10, p. 3203-3213 How to Cite?
AbstractComputational discovery of cis-regulatory elements remains challenging. To cope with the high false positives, evolutionary conservation is routinely used. However, conservation is only one of the attributes of cis-regulatory elements and is neither necessary nor sufficient. Here, we assess two additional attributes - positional and inter-motif distance specificity - that are critical for interactions between transcription factors. We first show that for a greater than expected fraction of known motifs, the genes that contain the motifs in their promoters in a position-specific or distancespecific manner are related, both in function and/or in expression pattern. We then use the position and distance specificity to discover novel motifs. Our work highlights the importance of distance and position specificity, in addition to the evolutionary conservation, in discovering cis-regulatory motifs. © 2007 The Author(s).
Persistent Identifierhttp://hdl.handle.net/10722/147563
ISSN
2015 Impact Factor: 9.202
2015 SCImago Journal Rankings: 7.458
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorVardhanabhuti, Sen_US
dc.contributor.authorWang, Jen_US
dc.contributor.authorHannenhalli, Sen_US
dc.date.accessioned2012-05-29T06:04:38Z-
dc.date.available2012-05-29T06:04:38Z-
dc.date.issued2007en_US
dc.identifier.citationNucleic Acids Research, 2007, v. 35 n. 10, p. 3203-3213en_US
dc.identifier.issn0305-1048en_US
dc.identifier.urihttp://hdl.handle.net/10722/147563-
dc.description.abstractComputational discovery of cis-regulatory elements remains challenging. To cope with the high false positives, evolutionary conservation is routinely used. However, conservation is only one of the attributes of cis-regulatory elements and is neither necessary nor sufficient. Here, we assess two additional attributes - positional and inter-motif distance specificity - that are critical for interactions between transcription factors. We first show that for a greater than expected fraction of known motifs, the genes that contain the motifs in their promoters in a position-specific or distancespecific manner are related, both in function and/or in expression pattern. We then use the position and distance specificity to discover novel motifs. Our work highlights the importance of distance and position specificity, in addition to the evolutionary conservation, in discovering cis-regulatory motifs. © 2007 The Author(s).en_US
dc.languageengen_US
dc.publisherOxford University Press. The Journal's web site is located at http://nar.oxfordjournals.org/en_US
dc.relation.ispartofNucleic Acids Researchen_US
dc.subject.meshAnimalsen_US
dc.subject.meshBase Sequenceen_US
dc.subject.meshBinding Sitesen_US
dc.subject.meshComputational Biologyen_US
dc.subject.meshConserved Sequenceen_US
dc.subject.meshEvolution, Molecularen_US
dc.subject.meshGene Expressionen_US
dc.subject.meshHumansen_US
dc.subject.meshMiceen_US
dc.subject.meshPromoter Regions, Geneticen_US
dc.subject.meshSequence Analysis, Dnaen_US
dc.subject.meshTranscription Factors - Metabolismen_US
dc.titlePosition and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservationen_US
dc.typeArticleen_US
dc.identifier.emailWang, J:junwen@hkucc.hku.hken_US
dc.identifier.authorityWang, J=rp00280en_US
dc.description.naturelink_to_subscribed_fulltexten_US
dc.identifier.doi10.1093/nar/gkm201en_US
dc.identifier.pmid17452354en_US
dc.identifier.scopuseid_2-s2.0-34250896139en_US
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-34250896139&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume35en_US
dc.identifier.issue10en_US
dc.identifier.spage3203en_US
dc.identifier.epage3213en_US
dc.identifier.isiWOS:000247817300004-
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridVardhanabhuti, S=16647990600en_US
dc.identifier.scopusauthoridWang, J=8950599500en_US
dc.identifier.scopusauthoridHannenhalli, S=6603889650en_US
dc.identifier.citeulike1379549-

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