Predicting the binding preference of transcription factors to individual DNA k-mers
Identifieur interne : 002959 ( Main/Exploration ); précédent : 002958; suivant : 002960Predicting 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.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : DNA, Transcription Factors.
- chemical , metabolism : DNA, Transcription Factors.
- methods : Computational Biology, Sequence Analysis, DNA.
- Binding Sites.
Abstract
Url:
DOI: 10.1093/bioinformatics/btn645
PubMed: 19088121
PubMed Central: 2666811
Affiliations:
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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="4"><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><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></affiliation></author><author><name sortKey="Badis, Gwenael" sort="Badis, Gwenael" uniqKey="Badis G" first="Gwenael" last="Badis">Gwenael Badis</name><affiliation wicri:level="4"><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><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></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="2"><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><placeName><region type="state">Massachusetts</region></placeName></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="4"><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><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></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="4"><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><orgName type="university">Université de Toronto</orgName><placeName><settlement type="city">Toronto</settlement><region type="state">Ontario</region></placeName></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><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="KwdFr" xml:lang="fr"><term>ADN ()</term><term>ADN (métabolisme)</term><term>Analyse de séquence d'ADN ()</term><term>Biologie informatique ()</term><term>Facteurs de transcription ()</term><term>Facteurs de transcription (métabolisme)</term><term>Sites de fixation</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" qualifier="métabolisme" xml:lang="fr"><term>ADN</term><term>Facteurs de transcription</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN</term><term>Analyse de séquence d'ADN</term><term>Biologie informatique</term><term>Facteurs de transcription</term><term>Sites de fixation</term></keywords></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><affiliations><list><country><li>Canada</li><li>États-Unis</li></country><region><li>Massachusetts</li><li>Ontario</li></region><settlement><li>Toronto</li></settlement><orgName><li>Université de Toronto</li></orgName></list><tree><noCountry><name sortKey="Alleyne, Trevis M" sort="Alleyne, Trevis M" uniqKey="Alleyne T" first="Trevis M." last="Alleyne">Trevis M. Alleyne</name><name sortKey="Talukder, Shaheynoor" sort="Talukder, Shaheynoor" uniqKey="Talukder S" first="Shaheynoor" last="Talukder">Shaheynoor Talukder</name></noCountry><country name="Canada"><region name="Ontario"><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></region><name sortKey="Badis, Gwenael" sort="Badis, Gwenael" uniqKey="Badis G" first="Gwenael" last="Badis">Gwenael Badis</name><name sortKey="Hughes, Timothy R" sort="Hughes, Timothy R" uniqKey="Hughes T" first="Timothy R." last="Hughes">Timothy R. Hughes</name><name sortKey="Morris, Quaid D" sort="Morris, Quaid D" uniqKey="Morris Q" first="Quaid D." last="Morris">Quaid D. Morris</name></country><country name="États-Unis"><region name="Massachusetts"><name sortKey="Berger, Michael F" sort="Berger, Michael F" uniqKey="Berger M" first="Michael F." last="Berger">Michael F. Berger</name></region><name sortKey="Berger, Michael F" sort="Berger, Michael F" uniqKey="Berger M" first="Michael F." last="Berger">Michael F. Berger</name><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L." last="Bulyk">Martha L. Bulyk</name><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L." last="Bulyk">Martha L. Bulyk</name><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L." last="Bulyk">Martha L. Bulyk</name><name sortKey="Bulyk, Martha L" sort="Bulyk, Martha L" uniqKey="Bulyk M" first="Martha L." last="Bulyk">Martha L. Bulyk</name><name sortKey="Gehrke, Andrew R" sort="Gehrke, Andrew R" uniqKey="Gehrke A" first="Andrew R." last="Gehrke">Andrew R. Gehrke</name><name sortKey="Philippakis, Anthony A" sort="Philippakis, Anthony A" uniqKey="Philippakis A" first="Anthony A." last="Philippakis">Anthony A. Philippakis</name><name sortKey="Philippakis, Anthony A" sort="Philippakis, Anthony A" uniqKey="Philippakis A" first="Anthony A." last="Philippakis">Anthony A. Philippakis</name><name sortKey="Philippakis, Anthony A" sort="Philippakis, Anthony A" uniqKey="Philippakis A" first="Anthony A." last="Philippakis">Anthony A. Philippakis</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Main/Exploration
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 002959 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd -nk 002959 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Main
|étape= Exploration
|type= RBID
|clé= PMC:2666811
|texte= Predicting the binding preference of transcription factors to individual DNA k-mers
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Main/Exploration/RBID.i -Sk "pubmed:19088121" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |