Predicting the binding preference of transcription factors to individual DNA k-mers.
Identifieur interne : 002053 ( PubMed/Corpus ); précédent : 002052; suivant : 002054Predicting the binding preference of transcription factors to individual DNA k-mers.
Auteurs : Trevis M. Alleyne ; Lourdes Pe A-Castillo ; Gwenael Badis ; Shaheynoor Talukder ; Michael F. Berger ; Andrew R. Gehrke ; Anthony A. Philippakis ; Martha L. Bulyk ; Quaid D. Morris ; Timothy R. HughesSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2009.
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, Transcription Factors.
- chemical , metabolism : DNA, Transcription Factors.
- methods : Computational Biology, Sequence Analysis, DNA.
- Binding Sites.
Abstract
Recognition of specific DNA sequences is a central mechanism by which transcription factors (TFs) control gene expression. Many TF-binding preferences, however, are unknown or poorly characterized, in part due to the difficulty associated with determining their specificity experimentally, and an incomplete understanding of the mechanisms governing sequence specificity. New techniques that estimate the affinity of TFs to all possible k-mers provide a new opportunity to study DNA-protein interaction mechanisms, and may facilitate inference of binding preferences for members of a given TF family when such information is available for other family members.
DOI: 10.1093/bioinformatics/btn645
PubMed: 19088121
Links to Exploration step
pubmed:19088121Le document en format XML
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Alleyne</name><affiliation><nlm:affiliation>Department of Molecular Genetics, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Pe A Castillo, Lourdes" sort="Pe A Castillo, Lourdes" uniqKey="Pe A Castillo L" first="Lourdes" last="Pe A-Castillo">Lourdes Pe A-Castillo</name></author><author><name sortKey="Badis, Gwenael" sort="Badis, Gwenael" uniqKey="Badis G" first="Gwenael" last="Badis">Gwenael Badis</name></author><author><name sortKey="Talukder, Shaheynoor" sort="Talukder, Shaheynoor" uniqKey="Talukder S" first="Shaheynoor" last="Talukder">Shaheynoor Talukder</name></author><author><name sortKey="Berger, Michael F" sort="Berger, Michael F" uniqKey="Berger M" first="Michael F" last="Berger">Michael F. Berger</name></author><author><name sortKey="Gehrke, Andrew R" sort="Gehrke, Andrew R" uniqKey="Gehrke A" first="Andrew R" last="Gehrke">Andrew R. Gehrke</name></author><author><name sortKey="Philippakis, Anthony A" sort="Philippakis, Anthony A" uniqKey="Philippakis A" first="Anthony A" last="Philippakis">Anthony A. Philippakis</name></author><author><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L" last="Bulyk">Martha L. Bulyk</name></author><author><name sortKey="Morris, Quaid D" sort="Morris, Quaid D" uniqKey="Morris Q" first="Quaid D" last="Morris">Quaid D. Morris</name></author><author><name sortKey="Hughes, Timothy R" sort="Hughes, Timothy R" uniqKey="Hughes T" first="Timothy R" last="Hughes">Timothy R. Hughes</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2009">2009</date><idno type="RBID">pubmed:19088121</idno><idno type="pmid">19088121</idno><idno type="doi">10.1093/bioinformatics/btn645</idno><idno type="wicri:Area/PubMed/Corpus">002053</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002053</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Predicting the binding preference of transcription factors to individual DNA k-mers.</title><author><name sortKey="Alleyne, Trevis M" sort="Alleyne, Trevis M" uniqKey="Alleyne T" first="Trevis M" last="Alleyne">Trevis M. Alleyne</name><affiliation><nlm:affiliation>Department of Molecular Genetics, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Pe A Castillo, Lourdes" sort="Pe A Castillo, Lourdes" uniqKey="Pe A Castillo L" first="Lourdes" last="Pe A-Castillo">Lourdes Pe A-Castillo</name></author><author><name sortKey="Badis, Gwenael" sort="Badis, Gwenael" uniqKey="Badis G" first="Gwenael" last="Badis">Gwenael Badis</name></author><author><name sortKey="Talukder, Shaheynoor" sort="Talukder, Shaheynoor" uniqKey="Talukder S" first="Shaheynoor" last="Talukder">Shaheynoor Talukder</name></author><author><name sortKey="Berger, Michael F" sort="Berger, Michael F" uniqKey="Berger M" first="Michael F" last="Berger">Michael F. Berger</name></author><author><name sortKey="Gehrke, Andrew R" sort="Gehrke, Andrew R" uniqKey="Gehrke A" first="Andrew R" last="Gehrke">Andrew R. Gehrke</name></author><author><name sortKey="Philippakis, Anthony A" sort="Philippakis, Anthony A" uniqKey="Philippakis A" first="Anthony A" last="Philippakis">Anthony A. Philippakis</name></author><author><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L" last="Bulyk">Martha L. Bulyk</name></author><author><name sortKey="Morris, Quaid D" sort="Morris, Quaid D" uniqKey="Morris Q" first="Quaid D" last="Morris">Quaid D. Morris</name></author><author><name sortKey="Hughes, Timothy R" sort="Hughes, Timothy R" uniqKey="Hughes T" first="Timothy R" last="Hughes">Timothy R. Hughes</name></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites</term><term>Computational Biology (methods)</term><term>DNA (chemistry)</term><term>DNA (metabolism)</term><term>Sequence Analysis, DNA (methods)</term><term>Transcription Factors (chemistry)</term><term>Transcription Factors (metabolism)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>DNA</term><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Recognition of specific DNA sequences is a central mechanism by which transcription factors (TFs) control gene expression. Many TF-binding preferences, however, are unknown or poorly characterized, in part due to the difficulty associated with determining their specificity experimentally, and an incomplete understanding of the mechanisms governing sequence specificity. New techniques that estimate the affinity of TFs to all possible k-mers provide a new opportunity to study DNA-protein interaction mechanisms, and may facilitate inference of binding preferences for members of a given TF family when such information is available for other family members.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19088121</PMID><DateCompleted><Year>2009</Year><Month>05</Month><Day>18</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>25</Volume><Issue>8</Issue><PubDate><Year>2009</Year><Month>Apr</Month><Day>15</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Predicting the binding preference of transcription factors to individual DNA k-mers.</ArticleTitle><Pagination><MedlinePgn>1012-8</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btn645</ELocationID><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">Recognition of specific DNA sequences is a central mechanism by which transcription factors (TFs) control gene expression. Many TF-binding preferences, however, are unknown or poorly characterized, in part due to the difficulty associated with determining their specificity experimentally, and an incomplete understanding of the mechanisms governing sequence specificity. New techniques that estimate the affinity of TFs to all possible k-mers provide a new opportunity to study DNA-protein interaction mechanisms, and may facilitate inference of binding preferences for members of a given TF family when such information is available for other family members.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We employed a new dataset consisting of the relative preferences of mouse homeodomains for all eight-base DNA sequences in order to ask how well we can predict the binding profiles of homeodomains when only their protein sequences are given. We evaluated a panel of standard statistical inference techniques, as well as variations of the protein features considered. Nearest neighbour among functionally important residues emerged among the most effective methods. Our results underscore the complexity of TF-DNA recognition, and suggest a rational approach for future analyses of TF families.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Alleyne</LastName><ForeName>Trevis M</ForeName><Initials>TM</Initials><AffiliationInfo><Affiliation>Department of Molecular Genetics, Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Peña-Castillo</LastName><ForeName>Lourdes</ForeName><Initials>L</Initials></Author><Author ValidYN="Y"><LastName>Badis</LastName><ForeName>Gwenael</ForeName><Initials>G</Initials></Author><Author ValidYN="Y"><LastName>Talukder</LastName><ForeName>Shaheynoor</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Berger</LastName><ForeName>Michael F</ForeName><Initials>MF</Initials></Author><Author ValidYN="Y"><LastName>Gehrke</LastName><ForeName>Andrew R</ForeName><Initials>AR</Initials></Author><Author ValidYN="Y"><LastName>Philippakis</LastName><ForeName>Anthony A</ForeName><Initials>AA</Initials></Author><Author ValidYN="Y"><LastName>Bulyk</LastName><ForeName>Martha L</ForeName><Initials>ML</Initials></Author><Author ValidYN="Y"><LastName>Morris</LastName><ForeName>Quaid D</ForeName><Initials>QD</Initials></Author><Author ValidYN="Y"><LastName>Hughes</LastName><ForeName>Timothy R</ForeName><Initials>TR</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><Agency>Howard Hughes Medical Institute</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D003160">Comparative Study</PublicationType><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2008</Year><Month>12</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</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="D001665" MajorTopicYN="N">Binding Sites</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019295" MajorTopicYN="N">Computational Biology</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D004247" MajorTopicYN="N">DNA</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D017422" MajorTopicYN="N">Sequence Analysis, DNA</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2008</Year><Month>12</Month><Day>18</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2008</Year><Month>12</Month><Day>18</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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