A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites
Identifieur interne : 000477 ( Ncbi/Checkpoint ); précédent : 000476; suivant : 000478A graph-based motif detection algorithm models complex nucleotide dependencies in transcription factor binding sites
Auteurs : Brian T. Naughton ; Eugene Fratkin ; Serafim Batzoglou ; Douglas L. BrutlagSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2006.
Descripteurs français
- KwdFr :
- MESH :
- analyse : Nucléotides.
- génétique : Saccharomyces cerevisiae.
- métabolisme : Facteurs de transcription.
- Algorithmes, Analyse de séquence d'ADN, Expression des gènes, Humains, Modèles génétiques, Modèles statistiques, Sites de fixation, Éléments de régulation transcriptionnelle.
English descriptors
- KwdEn :
- MESH :
- chemical , analysis : Nucleotides.
- genetics : Saccharomyces cerevisiae.
- chemical , metabolism : Transcription Factors.
- methods : Sequence Analysis, DNA.
- Algorithms, Binding Sites, Gene Expression, Humans, Models, Genetic, Models, Statistical, Regulatory Elements, Transcriptional.
Abstract
Given a set of known binding sites for a specific transcription factor, it is possible to build a model of the transcription factor binding site, usually called a motif model, and use this model to search for other sites that bind the same transcription factor. Typically, this search is performed using a position-specific scoring matrix (PSSM), also known as a position weight matrix. In this paper we analyze a set of eukaryotic transcription factor binding sites and show that there is extensive clustering of similar
Url:
DOI: 10.1093/nar/gkl585
PubMed: 17041233
PubMed Central: 1635261
Affiliations:
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Naughton</name></author><author><name sortKey="Fratkin, Eugene" sort="Fratkin, Eugene" uniqKey="Fratkin E" first="Eugene" last="Fratkin">Eugene Fratkin</name></author><author><name sortKey="Batzoglou, Serafim" sort="Batzoglou, Serafim" uniqKey="Batzoglou S" first="Serafim" last="Batzoglou">Serafim Batzoglou</name></author><author><name sortKey="Brutlag, Douglas L" sort="Brutlag, Douglas L" uniqKey="Brutlag D" first="Douglas L." last="Brutlag">Douglas L. Brutlag</name></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2006">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Binding Sites</term><term>Gene Expression</term><term>Humans</term><term>Models, Genetic</term><term>Models, Statistical</term><term>Nucleotides (analysis)</term><term>Regulatory Elements, Transcriptional</term><term>Saccharomyces cerevisiae (genetics)</term><term>Sequence Analysis, DNA (methods)</term><term>Transcription Factors (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN ()</term><term>Expression des gènes</term><term>Facteurs de transcription (métabolisme)</term><term>Humains</term><term>Modèles génétiques</term><term>Modèles statistiques</term><term>Nucléotides (analyse)</term><term>Saccharomyces cerevisiae (génétique)</term><term>Sites de fixation</term><term>Éléments de régulation transcriptionnelle</term></keywords><keywords scheme="MESH" type="chemical" qualifier="analysis" xml:lang="en"><term>Nucleotides</term></keywords><keywords scheme="MESH" qualifier="analyse" xml:lang="fr"><term>Nucléotides</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Saccharomyces cerevisiae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Saccharomyces cerevisiae</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Facteurs de transcription</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Binding Sites</term><term>Gene Expression</term><term>Humans</term><term>Models, Genetic</term><term>Models, Statistical</term><term>Regulatory Elements, Transcriptional</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Expression des gènes</term><term>Humains</term><term>Modèles génétiques</term><term>Modèles statistiques</term><term>Sites de fixation</term><term>Éléments de régulation transcriptionnelle</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Given a set of known binding sites for a specific transcription factor, it is possible to build a model of the transcription factor binding site, usually called a motif model, and use this model to search for other sites that bind the same transcription factor. Typically, this search is performed using a position-specific scoring matrix (PSSM), also known as a position weight matrix. In this paper we analyze a set of eukaryotic transcription factor binding sites and show that there is extensive clustering of similar <italic>k</italic>-mers in eukaryotic motifs, owing to both functional and evolutionary constraints. The apparent limitations of probabilistic models in representing complex nucleotide dependencies lead us to a graph-based representation of motifs. When deciding whether a candidate <italic>k</italic>-mer is part of a motif or not, we base our decision not on how well the <italic>k</italic>-mer conforms to a model of the motif as a whole, but how similar it is to specific, known <italic>k</italic>-mers in the motif. We elucidate the reasons why we expect graph-based methods to perform well on motif data. Our MotifScan algorithm shows greatly improved performance over the prevalent PSSM-based method for the detection of eukaryotic motifs.</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><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Batzoglou, Serafim" sort="Batzoglou, Serafim" uniqKey="Batzoglou S" first="Serafim" last="Batzoglou">Serafim Batzoglou</name><name sortKey="Brutlag, Douglas L" sort="Brutlag, Douglas L" uniqKey="Brutlag D" first="Douglas L." last="Brutlag">Douglas L. Brutlag</name><name sortKey="Fratkin, Eugene" sort="Fratkin, Eugene" uniqKey="Fratkin E" first="Eugene" last="Fratkin">Eugene Fratkin</name><name sortKey="Naughton, Brian T" sort="Naughton, Brian T" uniqKey="Naughton B" first="Brian T." last="Naughton">Brian T. Naughton</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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