MotifClick: prediction of cis-regulatory binding sites via merging cliques.
Identifieur interne : 001E68 ( PubMed/Curation ); précédent : 001E67; suivant : 001E69MotifClick: prediction of cis-regulatory binding sites via merging cliques.
Auteurs : Shaoqiang Zhang [États-Unis] ; Shan Li ; Meng Niu ; Phuc T. Pham ; Zhengchang SuSource :
- BMC bioinformatics [ 1471-2105 ] ; 2011.
Descripteurs français
- KwdFr :
- MESH :
- génétique : Drosophila melanogaster, Escherichia coli, Saccharomyces cerevisiae.
- métabolisme : ADN, Facteurs de transcription.
- Algorithmes, Animaux, Sites de fixation, Séquence nucléotidique.
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : DNA, Transcription Factors.
- genetics : Drosophila melanogaster, Escherichia coli, Saccharomyces cerevisiae.
- Algorithms, Animals, Base Sequence, Binding Sites.
Abstract
Although dozens of algorithms and tools have been developed to find a set of cis-regulatory binding sites called a motif in a set of intergenic sequences using various approaches, most of these tools focus on identifying binding sites that are significantly different from their background sequences. However, some motifs may have a similar nucleotide distribution to that of their background sequences. Therefore, such binding sites can be missed by these tools.
DOI: 10.1186/1471-2105-12-238
PubMed: 21679436
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Pham</name></author><author><name sortKey="Su, Zhengchang" sort="Su, Zhengchang" uniqKey="Su Z" first="Zhengchang" last="Su">Zhengchang Su</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2011">2011</date><idno type="RBID">pubmed:21679436</idno><idno type="pmid">21679436</idno><idno type="doi">10.1186/1471-2105-12-238</idno><idno type="wicri:Area/PubMed/Corpus">001E68</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001E68</idno><idno type="wicri:Area/PubMed/Curation">001E68</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001E68</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">MotifClick: prediction of cis-regulatory binding sites via merging cliques.</title><author><name sortKey="Zhang, Shaoqiang" sort="Zhang, Shaoqiang" uniqKey="Zhang S" first="Shaoqiang" last="Zhang">Shaoqiang Zhang</name><affiliation wicri:level="1"><nlm:affiliation>Department of Bioinformatics and Genomics, Center for Bioinformatics Research, the University of North Carolina at Charlotte, 28223, USA.</nlm:affiliation><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Bioinformatics and Genomics, Center for Bioinformatics Research, the University of North Carolina at Charlotte, 28223</wicri:regionArea></affiliation></author><author><name sortKey="Li, Shan" sort="Li, Shan" uniqKey="Li S" first="Shan" last="Li">Shan Li</name></author><author><name sortKey="Niu, Meng" sort="Niu, Meng" uniqKey="Niu M" first="Meng" last="Niu">Meng Niu</name></author><author><name sortKey="Pham, Phuc T" sort="Pham, Phuc T" uniqKey="Pham P" first="Phuc T" last="Pham">Phuc T. Pham</name></author><author><name sortKey="Su, Zhengchang" sort="Su, Zhengchang" uniqKey="Su Z" first="Zhengchang" last="Su">Zhengchang Su</name></author></analytic><series><title level="j">BMC bioinformatics</title><idno type="eISSN">1471-2105</idno><imprint><date when="2011" type="published">2011</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Base Sequence</term><term>Binding Sites</term><term>DNA (metabolism)</term><term>Drosophila melanogaster (genetics)</term><term>Escherichia coli (genetics)</term><term>Saccharomyces cerevisiae (genetics)</term><term>Transcription Factors (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN (métabolisme)</term><term>Algorithmes</term><term>Animaux</term><term>Drosophila melanogaster (génétique)</term><term>Escherichia coli (génétique)</term><term>Facteurs de transcription (métabolisme)</term><term>Saccharomyces cerevisiae (génétique)</term><term>Sites de fixation</term><term>Séquence nucléotidique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Drosophila melanogaster</term><term>Escherichia coli</term><term>Saccharomyces cerevisiae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Drosophila melanogaster</term><term>Escherichia coli</term><term>Saccharomyces cerevisiae</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>ADN</term><term>Facteurs de transcription</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Animals</term><term>Base Sequence</term><term>Binding Sites</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Animaux</term><term>Sites de fixation</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Although dozens of algorithms and tools have been developed to find a set of cis-regulatory binding sites called a motif in a set of intergenic sequences using various approaches, most of these tools focus on identifying binding sites that are significantly different from their background sequences. However, some motifs may have a similar nucleotide distribution to that of their background sequences. Therefore, such binding sites can be missed by these tools.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">21679436</PMID><DateCompleted><Year>2011</Year><Month>10</Month><Day>24</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>01</Day></DateRevised><Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2105</ISSN><JournalIssue CitedMedium="Internet"><Volume>12</Volume><PubDate><Year>2011</Year><Month>Jun</Month><Day>16</Day></PubDate></JournalIssue><Title>BMC bioinformatics</Title><ISOAbbreviation>BMC Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>MotifClick: prediction of cis-regulatory binding sites via merging cliques.</ArticleTitle><Pagination><MedlinePgn>238</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1186/1471-2105-12-238</ELocationID><Abstract><AbstractText Label="BACKGROUND" NlmCategory="BACKGROUND">Although dozens of algorithms and tools have been developed to find a set of cis-regulatory binding sites called a motif in a set of intergenic sequences using various approaches, most of these tools focus on identifying binding sites that are significantly different from their background sequences. However, some motifs may have a similar nucleotide distribution to that of their background sequences. Therefore, such binding sites can be missed by these tools.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">Here, we present a graph-based polynomial-time algorithm, MotifClick, for the prediction of cis-regulatory binding sites, in particular, those that have a similar nucleotide distribution to that of their background sequences. To find binding sites with length k, we construct a graph using some 2(k-1)-mers in the input sequences as the vertices, and connect two vertices by an edge if the maximum number of matches of the local gapless alignments between the two 2(k-1)-mers is greater than a cutoff value. We identify a motif as a set of similar k-mers from a merged group of maximum cliques associated with some vertices.</AbstractText><AbstractText Label="CONCLUSIONS" NlmCategory="CONCLUSIONS">When evaluated on both synthetic and real datasets of prokaryotes and eukaryotes, MotifClick outperforms existing leading motif-finding tools for prediction accuracy and balancing the prediction sensitivity and specificity in general. In particular, when the distribution of nucleotides of binding sites is similar to that of their background sequences, MotifClick is more likely to identify the binding sites than the other tools.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Zhang</LastName><ForeName>Shaoqiang</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Department of Bioinformatics and Genomics, Center for Bioinformatics Research, the University of North Carolina at Charlotte, 28223, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Shan</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Niu</LastName><ForeName>Meng</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Pham</LastName><ForeName>Phuc T</ForeName><Initials>PT</Initials></Author><Author ValidYN="Y"><LastName>Su</LastName><ForeName>Zhengchang</ForeName><Initials>Z</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2011</Year><Month>06</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>BMC Bioinformatics</MedlineTA><NlmUniqueID>100965194</NlmUniqueID><ISSNLinking>1471-2105</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance></Chemical><Chemical><RegistryNumber>9007-49-2</RegistryNumber><NameOfSubstance UI="D004247">DNA</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="Y">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004331" MajorTopicYN="N">Drosophila melanogaster</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004926" MajorTopicYN="N">Escherichia coli</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012441" MajorTopicYN="N">Saccharomyces cerevisiae</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2010</Year><Month>12</Month><Day>23</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2011</Year><Month>06</Month><Day>16</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2011</Year><Month>6</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2011</Year><Month>6</Month><Day>18</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2011</Year><Month>10</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>epublish</PublicationStatus><ArticleIdList><ArticleId 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