Predicting the binding preference of transcription factors to individual DNA k-mers
Identifieur interne : 000938 ( Pmc/Curation ); précédent : 000937; suivant : 000939Predicting the binding preference of transcription factors to individual DNA k-mers
Auteurs : Trevis M. Alleyne ; Lourdes Pe A-Castillo [Canada] ; Gwenael Badis [Canada] ; Shaheynoor Talukder ; Michael F. Berger [États-Unis] ; Andrew R. Gehrke [États-Unis] ; Anthony A. Philippakis [États-Unis] ; Martha L. Bulyk [États-Unis] ; Quaid D. Morris [Canada] ; Timothy R. Hughes [Canada]Source :
- Bioinformatics [ 1367-4803 ] ; 2008.
Abstract
Url:
DOI: 10.1093/bioinformatics/btn645
PubMed: 19088121
PubMed Central: 2666811
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Alleyne</name><affiliation><nlm:aff id="AFF1">Department of Molecular Genetics,</nlm:aff></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><affiliation wicri:level="1"><nlm:aff id="AFF1">Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada,</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1</wicri:regionArea></affiliation></author><author><name sortKey="Badis, Gwenael" sort="Badis, Gwenael" uniqKey="Badis G" first="Gwenael" last="Badis">Gwenael Badis</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada,</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1</wicri:regionArea></affiliation></author><author><name sortKey="Talukder, Shaheynoor" sort="Talukder, Shaheynoor" uniqKey="Talukder S" first="Shaheynoor" last="Talukder">Shaheynoor Talukder</name><affiliation><nlm:aff id="AFF1">Department of Molecular Genetics,</nlm:aff></affiliation></author><author><name sortKey="Berger, Michael F" sort="Berger, Michael F" uniqKey="Berger M" first="Michael F." last="Berger">Michael F. Berger</name><affiliation wicri:level="2"><nlm:aff id="AFF1">Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115,</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="AFF1">Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138,</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Committee on Higher Degrees in Biophysics, Harvard University, Cambridge</wicri:cityArea></affiliation></author><author><name sortKey="Gehrke, Andrew R" sort="Gehrke, Andrew R" uniqKey="Gehrke A" first="Andrew R." last="Gehrke">Andrew R. Gehrke</name><affiliation wicri:level="2"><nlm:aff id="AFF1">Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115,</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston</wicri:cityArea></affiliation></author><author><name sortKey="Philippakis, Anthony A" sort="Philippakis, Anthony A" uniqKey="Philippakis A" first="Anthony A." last="Philippakis">Anthony A. Philippakis</name><affiliation wicri:level="2"><nlm:aff id="AFF1">Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115,</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="AFF1">Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138,</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Committee on Higher Degrees in Biophysics, Harvard University, Cambridge</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="AFF1">Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston</wicri:cityArea></affiliation></author><author><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L." last="Bulyk">Martha L. Bulyk</name><affiliation wicri:level="2"><nlm:aff id="AFF1">Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115,</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff id="AFF1">Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138,</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Committee on Higher Degrees in Biophysics, Harvard University, Cambridge</wicri:cityArea></affiliation><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="AFF1">Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Massachusetts</region></placeName><wicri:cityArea>Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston</wicri:cityArea></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115</wicri:regionArea></affiliation></author><author><name sortKey="Morris, Quaid D" sort="Morris, Quaid D" uniqKey="Morris Q" first="Quaid D." last="Morris">Quaid D. Morris</name><affiliation><nlm:aff id="AFF1">Department of Molecular Genetics,</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF1">Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada,</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1</wicri:regionArea></affiliation></author><author><name sortKey="Hughes, Timothy R" sort="Hughes, Timothy R" uniqKey="Hughes T" first="Timothy R." last="Hughes">Timothy R. Hughes</name><affiliation><nlm:aff id="AFF1">Department of Molecular Genetics,</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF1">Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada,</nlm:aff><country xml:lang="fr">Canada</country><wicri:regionArea>Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1</wicri:regionArea></affiliation></author></analytic><series><title level="j">Bioinformatics</title><idno type="ISSN">1367-4803</idno><idno type="eISSN">1460-2059</idno><imprint><date when="2008">2008</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><bold>Motivation:</bold> 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 <italic>k</italic>-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.</p><p><bold>Results:</bold> 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.</p><p><bold>Contact:</bold> <email>t.hughes@utorotno.ca</email></p><p><bold>Supplementary information:</bold> <ext-link ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/cgi/content/full/btn645/DC1">Supplementary data</ext-link> are available at <italic>Bioinformatics</italic> online.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><pmc article-type="research-article" xml:lang="EN"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Bioinformatics</journal-id><journal-id journal-id-type="publisher-id">bioinformatics</journal-id><journal-id journal-id-type="hwp">bioinfo</journal-id><journal-title>Bioinformatics</journal-title><issn pub-type="ppub">1367-4803</issn><issn pub-type="epub">1460-2059</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">19088121</article-id><article-id pub-id-type="pmc">2666811</article-id><article-id pub-id-type="doi">10.1093/bioinformatics/btn645</article-id><article-id pub-id-type="publisher-id">btn645</article-id><article-categories><subj-group subj-group-type="heading"><subject>Original Papers</subject><subj-group><subject>Gene Expression</subject></subj-group></subj-group></article-categories><title-group><article-title>Predicting the binding preference of transcription factors to individual DNA <italic>k</italic>-mers</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Alleyne</surname><given-names>Trevis M.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Peña-Castillo</surname><given-names>Lourdes</given-names></name><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Badis</surname><given-names>Gwenael</given-names></name><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Talukder</surname><given-names>Shaheynoor</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Berger</surname><given-names>Michael F.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>3</sup></xref><xref ref-type="aff" rid="AFF1"><sup>4</sup></xref></contrib><contrib contrib-type="author"><name><surname>Gehrke</surname><given-names>Andrew R.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Philippakis</surname><given-names>Anthony A.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>3</sup></xref><xref ref-type="aff" rid="AFF1"><sup>4</sup></xref><xref ref-type="aff" rid="AFF1"><sup>5</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bulyk</surname><given-names>Martha L.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>3</sup></xref><xref ref-type="aff" rid="AFF1"><sup>4</sup></xref><xref ref-type="aff" rid="AFF1"><sup>5</sup></xref><xref ref-type="aff" rid="AFF1"><sup>6</sup></xref></contrib><contrib contrib-type="author"><name><surname>Morris</surname><given-names>Quaid D.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Hughes</surname><given-names>Timothy R.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref><xref ref-type="corresp" rid="COR1">*</xref></contrib></contrib-group><aff id="AFF1"><sup>1</sup>Department of Molecular Genetics,<sup>2</sup>Banting and Best Department of Medical Research, University of Toronto, Toronto, ON M5S 3E1, Canada,<sup>3</sup>Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115,<sup>4</sup>Committee on Higher Degrees in Biophysics, Harvard University, Cambridge, MA 02138,<sup>5</sup>Harvard/MIT Division of Health Sciences and Technology (HST), Harvard Medical School, Boston, MA 02115 and<sup>6</sup>Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA</aff><author-notes><corresp id="COR1">*To whom correspondence should be addressed.</corresp><fn><p>Associate Editor: David Rocke</p></fn></author-notes><pub-date pub-type="ppub"><day>15</day><month>4</month><year>2009</year></pub-date><pub-date pub-type="epub"><day>16</day><month>12</month><year>2008</year></pub-date><pub-date pub-type="pmc-release"><day>16</day><month>12</month><year>2008</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>25</volume><issue>8</issue><fpage>1012</fpage><lpage>1018</lpage><history><date date-type="received"><day>10</day><month>8</month><year>2008</year></date><date date-type="rev-recd"><day>16</day><month>11</month><year>2008</year></date><date date-type="accepted"><day>11</day><month>12</month><year>2008</year></date></history><permissions><copyright-statement>© 2008 The Author(s)</copyright-statement><copyright-year>2008</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/2.0/uk/"><p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/2.0/uk/">http://creativecommons.org/licenses/by-nc/2.0/uk/</ext-link>) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</p></license></permissions><abstract><p><bold>Motivation:</bold> 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 <italic>k</italic>-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.</p><p><bold>Results:</bold> 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.</p><p><bold>Contact:</bold> <email>t.hughes@utorotno.ca</email></p><p><bold>Supplementary information:</bold> <ext-link ext-link-type="uri" xlink:href="http://bioinformatics.oxfordjournals.org/cgi/content/full/btn645/DC1">Supplementary data</ext-link> are available at <italic>Bioinformatics</italic> online.</p></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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HfdIndexSelect -h $EXPLOR_AREA/Data/Pmc/Curation/RBID.i -Sk "pubmed:19088121" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Pmc/Curation/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |