RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors.
Identifieur interne : 002B37 ( Main/Exploration ); précédent : 002B36; suivant : 002B38RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors.
Auteurs : Xiaoyu Chen [Canada] ; Timothy R. Hughes ; Quaid MorrisSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2007.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Transcription Factors.
- chemical , genetics : Transcription Factors.
- methods : Sequence Analysis, DNA.
- Algorithms, Amino Acid Motifs, Base Sequence, Binding Sites, Molecular Sequence Data, Protein Binding.
Abstract
The sequence specificity of DNA-binding proteins is typically represented as a position weight matrix in which each base position contributes independently to relative affinity. Assessment of the accuracy and broad applicability of this representation has been limited by the lack of extensive DNA-binding data. However, new microarray techniques, in which preferences for all possible K-mers are measured, enable a broad comparison of both motif representation and methods for motif discovery. Here, we consider the problem of accounting for all of the binding data in such experiments, rather than the highest affinity binding data. We introduce the RankMotif++, an algorithm designed for finding motifs whenever sequences are associated with a semi-quantitative measure of protein-DNA-binding affinity. RankMotif++ learns motif models by maximizing the likelihood of a set of binding preferences under a probabilistic model of how sequence binding affinity translates into binding preference observations. Because RankMotif++ makes few assumptions about the relationship between binding affinity and the semi-quantitative readout, it is applicable to a wide variety of experimental assays of DNA-binding preference.
DOI: 10.1093/bioinformatics/btm224
PubMed: 17646348
Affiliations:
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Le document en format XML
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Hughes</name></author><author><name sortKey="Morris, Quaid" sort="Morris, Quaid" uniqKey="Morris Q" first="Quaid" last="Morris">Quaid Morris</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2007">2007</date><idno type="RBID">pubmed:17646348</idno><idno type="pmid">17646348</idno><idno type="doi">10.1093/bioinformatics/btm224</idno><idno type="wicri:Area/PubMed/Corpus">002173</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002173</idno><idno type="wicri:Area/PubMed/Curation">002173</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002173</idno><idno type="wicri:Area/PubMed/Checkpoint">002039</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002039</idno><idno type="wicri:Area/Ncbi/Merge">000533</idno><idno type="wicri:Area/Ncbi/Curation">000533</idno><idno type="wicri:Area/Ncbi/Checkpoint">000533</idno><idno type="wicri:Area/Main/Merge">002B63</idno><idno type="wicri:Area/Main/Curation">002B37</idno><idno type="wicri:Area/Main/Exploration">002B37</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">RankMotif++: a motif-search algorithm that accounts for relative ranks of K-mers in binding transcription factors.</title><author><name sortKey="Chen, Xiaoyu" sort="Chen, Xiaoyu" uniqKey="Chen X" first="Xiaoyu" last="Chen">Xiaoyu Chen</name><affiliation wicri:level="4"><nlm:affiliation>Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada.</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Banting and Best Department of Medical Research, University of Toronto, Toronto, ON</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></author><author><name sortKey="Morris, Quaid" sort="Morris, Quaid" uniqKey="Morris Q" first="Quaid" last="Morris">Quaid Morris</name></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2007" type="published">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Amino Acid Motifs</term><term>Base Sequence</term><term>Binding Sites</term><term>Molecular Sequence Data</term><term>Protein Binding</term><term>Sequence Analysis, DNA (methods)</term><term>Transcription Factors (chemistry)</term><term>Transcription Factors (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN ()</term><term>Données de séquences moléculaires</term><term>Facteurs de transcription ()</term><term>Facteurs de transcription (génétique)</term><term>Liaison aux protéines</term><term>Motifs d'acides aminés</term><term>Sites de fixation</term><term>Séquence nucléotidique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Transcription Factors</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Transcription Factors</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Facteurs de transcription</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Amino Acid Motifs</term><term>Base Sequence</term><term>Binding Sites</term><term>Molecular Sequence Data</term><term>Protein Binding</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Analyse de séquence d'ADN</term><term>Données de séquences moléculaires</term><term>Facteurs de transcription</term><term>Liaison aux protéines</term><term>Motifs d'acides aminés</term><term>Sites de fixation</term><term>Séquence nucléotidique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The sequence specificity of DNA-binding proteins is typically represented as a position weight matrix in which each base position contributes independently to relative affinity. Assessment of the accuracy and broad applicability of this representation has been limited by the lack of extensive DNA-binding data. However, new microarray techniques, in which preferences for all possible K-mers are measured, enable a broad comparison of both motif representation and methods for motif discovery. Here, we consider the problem of accounting for all of the binding data in such experiments, rather than the highest affinity binding data. We introduce the RankMotif++, an algorithm designed for finding motifs whenever sequences are associated with a semi-quantitative measure of protein-DNA-binding affinity. RankMotif++ learns motif models by maximizing the likelihood of a set of binding preferences under a probabilistic model of how sequence binding affinity translates into binding preference observations. Because RankMotif++ makes few assumptions about the relationship between binding affinity and the semi-quantitative readout, it is applicable to a wide variety of experimental assays of DNA-binding preference.</div></front></TEI><affiliations><list><country><li>Canada</li></country><region><li>Ontario</li></region><settlement><li>Toronto</li></settlement><orgName><li>Université de Toronto</li></orgName></list><tree><noCountry><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" sort="Morris, Quaid" uniqKey="Morris Q" first="Quaid" last="Morris">Quaid Morris</name></noCountry><country name="Canada"><region name="Ontario"><name sortKey="Chen, Xiaoyu" sort="Chen, Xiaoyu" uniqKey="Chen X" first="Xiaoyu" last="Chen">Xiaoyu Chen</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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