Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features
Identifieur interne : 001C66 ( Main/Exploration ); précédent : 001C65; suivant : 001C67Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features
Auteurs : Mahmoud Ghandi [États-Unis] ; Dongwon Lee [États-Unis] ; Morteza Mohammad-Noori [Iran] ; Michael A. Beer [États-Unis]Source :
- PLoS Computational Biology [ 1553-734X ] ; 2014.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ADN (), Biologie informatique (), Immunoprécipitation de la chromatine, Machine à vecteur de support, Modèles génétiques, Oligonucléotides (génétique), Spécificité d'organe (génétique), Séquence nucléotidique, Séquences d'acides nucléiques régulatrices (génétique), Théorème de Bayes.
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Oligonucleotides.
- genetics : Organ Specificity, Regulatory Sequences, Nucleic Acid.
- methods : Computational Biology, Sequence Analysis, DNA.
- Base Sequence, Bayes Theorem, Chromatin Immunoprecipitation, Models, Genetic, Support Vector Machine.
Abstract
Oligomers of length
Url:
DOI: 10.1371/journal.pcbi.1003711
PubMed: 25033408
PubMed Central: 4102394
Affiliations:
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Beer</name><affiliation wicri:level="2"><nlm:aff id="aff1"><addr-line>Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="aff4"><addr-line>McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America</addr-line></nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author></analytic><series><title level="j">PLoS Computational Biology</title><idno type="ISSN">1553-734X</idno><idno type="eISSN">1553-7358</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Base Sequence</term><term>Bayes Theorem</term><term>Chromatin Immunoprecipitation</term><term>Computational Biology (methods)</term><term>Models, Genetic</term><term>Oligonucleotides (genetics)</term><term>Organ Specificity (genetics)</term><term>Regulatory Sequences, Nucleic Acid (genetics)</term><term>Sequence Analysis, DNA (methods)</term><term>Support Vector Machine</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN ()</term><term>Biologie informatique ()</term><term>Immunoprécipitation de la chromatine</term><term>Machine à vecteur de support</term><term>Modèles génétiques</term><term>Oligonucléotides (génétique)</term><term>Spécificité d'organe (génétique)</term><term>Séquence nucléotidique</term><term>Séquences d'acides nucléiques régulatrices (génétique)</term><term>Théorème de Bayes</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Oligonucleotides</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Organ Specificity</term><term>Regulatory Sequences, Nucleic Acid</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Oligonucléotides</term><term>Spécificité d'organe</term><term>Séquences d'acides nucléiques régulatrices</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>Base Sequence</term><term>Bayes Theorem</term><term>Chromatin Immunoprecipitation</term><term>Models, Genetic</term><term>Support Vector Machine</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term><term>Biologie informatique</term><term>Immunoprécipitation de la chromatine</term><term>Machine à vecteur de support</term><term>Modèles génétiques</term><term>Séquence nucléotidique</term><term>Théorème de Bayes</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><title>Abstract</title><p>Oligomers of length <italic>k</italic>, or <italic>k</italic>-mers, are convenient and widely used features for modeling the properties and functions of DNA and protein sequences. However, <italic>k</italic>-mers suffer from the inherent limitation that if the parameter <italic>k</italic> is increased to resolve longer features, the probability of observing any specific <italic>k</italic>-mer becomes very small, and <italic>k-</italic>mer counts approach a binary variable, with most <italic>k</italic>-mers absent and a few present once. Thus, any statistical learning approach using <italic>k</italic>-mers as features becomes susceptible to noisy training set <italic>k</italic>-mer frequencies once <italic>k</italic> becomes large. To address this problem, we introduce alternative feature sets using gapped <italic>k</italic>-mers, a new classifier, gkm-SVM, and a general method for robust estimation of <italic>k</italic>-mer frequencies. To make the method applicable to large-scale genome wide applications, we develop an efficient tree data structure for computing the kernel matrix. We show that compared to our original kmer-SVM and alternative approaches, our gkm-SVM predicts functional genomic regulatory elements and tissue specific enhancers with significantly improved accuracy, increasing the precision by up to a factor of two. We then show that gkm-SVM consistently outperforms kmer-SVM on human ENCODE ChIP-seq datasets, and further demonstrate the general utility of our method using a Naïve-Bayes classifier. Although developed for regulatory sequence analysis, these methods can be applied to any sequence classification problem.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Manolio, Ta" uniqKey="Manolio T">TA Manolio</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Maurano, Mt" uniqKey="Maurano M">MT Maurano</name></author><author><name sortKey="Humbert, R" uniqKey="Humbert R">R Humbert</name></author><author><name sortKey="Rynes, E" uniqKey="Rynes E">E Rynes</name></author><author><name sortKey="Thurman, Re" uniqKey="Thurman R">RE Thurman</name></author><author><name sortKey="Haugen, E" uniqKey="Haugen E">E Haugen</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Lee, D" uniqKey="Lee D">D Lee</name></author><author><name sortKey="Karchin, R" uniqKey="Karchin R">R Karchin</name></author><author><name sortKey="Beer, Ma" uniqKey="Beer M">MA 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Bailey</name></author><author><name sortKey="Noble, Ws" uniqKey="Noble W">WS Noble</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Sing, T" uniqKey="Sing T">T Sing</name></author><author><name sortKey="Sander, O" uniqKey="Sander O">O Sander</name></author><author><name sortKey="Beerenwinkel, N" uniqKey="Beerenwinkel N">N Beerenwinkel</name></author><author><name sortKey="Lengauer, T" uniqKey="Lengauer T">T Lengauer</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bryne, Jc" uniqKey="Bryne J">JC Bryne</name></author><author><name sortKey="Valen, E" uniqKey="Valen E">E Valen</name></author><author><name sortKey="Tang, M He" uniqKey="Tang M">M-HE Tang</name></author><author><name sortKey="Marstrand, T" uniqKey="Marstrand T">T Marstrand</name></author><author><name sortKey="Winther, O" uniqKey="Winther O">O Winther</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Iran</li><li>États-Unis</li></country><region><li>Maryland</li></region></list><tree><country name="États-Unis"><region name="Maryland"><name sortKey="Ghandi, Mahmoud" sort="Ghandi, Mahmoud" uniqKey="Ghandi M" first="Mahmoud" last="Ghandi">Mahmoud Ghandi</name></region><name sortKey="Beer, Michael A" sort="Beer, Michael A" uniqKey="Beer M" first="Michael A." last="Beer">Michael A. Beer</name><name sortKey="Beer, Michael A" sort="Beer, Michael A" uniqKey="Beer M" first="Michael A." last="Beer">Michael A. Beer</name><name sortKey="Lee, Dongwon" sort="Lee, Dongwon" uniqKey="Lee D" first="Dongwon" last="Lee">Dongwon Lee</name></country><country name="Iran"><noRegion><name sortKey="Mohammad Noori, Morteza" sort="Mohammad Noori, Morteza" uniqKey="Mohammad Noori M" first="Morteza" last="Mohammad-Noori">Morteza Mohammad-Noori</name></noRegion><name sortKey="Mohammad Noori, Morteza" sort="Mohammad Noori, Morteza" uniqKey="Mohammad Noori M" first="Morteza" last="Mohammad-Noori">Morteza Mohammad-Noori</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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