A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data
Identifieur interne : 000C79 ( Ncbi/Curation ); précédent : 000C78; suivant : 000C80A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data
Auteurs : Yaron Orenstein ; Ron ShamirSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2014.
Descripteurs français
- KwdFr :
- Analyse de séquence d'ADN, Analyse par réseau de protéines (), Animaux, Facteurs de transcription (métabolisme), Humains, Immunoprécipitation de la chromatine, Modèles biologiques, Oligonucléotides, Sites de fixation, Souris, Séquençage nucléotidique à haut débit, Technique SELEX (), Éléments de régulation transcriptionnelle.
- MESH :
- métabolisme : Facteurs de transcription.
- Analyse de séquence d'ADN, Analyse par réseau de protéines, Animaux, Humains, Immunoprécipitation de la chromatine, Modèles biologiques, Oligonucléotides, Sites de fixation, Souris, Séquençage nucléotidique à haut débit, Technique SELEX, Éléments de régulation transcriptionnelle.
English descriptors
- KwdEn :
- Animals, Binding Sites, Chromatin Immunoprecipitation, High-Throughput Nucleotide Sequencing, Humans, Mice, Models, Biological, Oligonucleotides, Protein Array Analysis (methods), Regulatory Elements, Transcriptional, SELEX Aptamer Technique (methods), Sequence Analysis, DNA, Transcription Factors (metabolism).
- MESH :
- chemical , metabolism : Transcription Factors.
- chemical : Oligonucleotides.
- methods : Protein Array Analysis, SELEX Aptamer Technique.
- Animals, Binding Sites, Chromatin Immunoprecipitation, High-Throughput Nucleotide Sequencing, Humans, Mice, Models, Biological, Regulatory Elements, Transcriptional, Sequence Analysis, DNA.
Abstract
Understanding gene regulation is a key challenge in today's biology. The new technologies of protein-binding microarrays (PBMs) and high-throughput SELEX (HT-SELEX) allow measurement of the binding intensities of one transcription factor (TF) to numerous synthetic double-stranded DNA sequences in a single experiment. Recently, Jolma
Url:
DOI: 10.1093/nar/gku117
PubMed: 24500199
PubMed Central: 4005680
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PMC:4005680Le document en format XML
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<sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data</title>
<author><name sortKey="Orenstein, Yaron" sort="Orenstein, Yaron" uniqKey="Orenstein Y" first="Yaron" last="Orenstein">Yaron Orenstein</name>
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<author><name sortKey="Shamir, Ron" sort="Shamir, Ron" uniqKey="Shamir R" first="Ron" last="Shamir">Ron Shamir</name>
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<series><title level="j">Nucleic Acids Research</title>
<idno type="ISSN">0305-1048</idno>
<idno type="eISSN">1362-4962</idno>
<imprint><date when="2014">2014</date>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term>
<term>Binding Sites</term>
<term>Chromatin Immunoprecipitation</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Humans</term>
<term>Mice</term>
<term>Models, Biological</term>
<term>Oligonucleotides</term>
<term>Protein Array Analysis (methods)</term>
<term>Regulatory Elements, Transcriptional</term>
<term>SELEX Aptamer Technique (methods)</term>
<term>Sequence Analysis, DNA</term>
<term>Transcription Factors (metabolism)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Analyse par réseau de protéines ()</term>
<term>Animaux</term>
<term>Facteurs de transcription (métabolisme)</term>
<term>Humains</term>
<term>Immunoprécipitation de la chromatine</term>
<term>Modèles biologiques</term>
<term>Oligonucléotides</term>
<term>Sites de fixation</term>
<term>Souris</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Technique SELEX ()</term>
<term>Éléments de régulation transcriptionnelle</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" type="chemical" xml:lang="en"><term>Oligonucleotides</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Protein Array Analysis</term>
<term>SELEX Aptamer Technique</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Facteurs de transcription</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Animals</term>
<term>Binding Sites</term>
<term>Chromatin Immunoprecipitation</term>
<term>High-Throughput Nucleotide Sequencing</term>
<term>Humans</term>
<term>Mice</term>
<term>Models, Biological</term>
<term>Regulatory Elements, Transcriptional</term>
<term>Sequence Analysis, DNA</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Analyse par réseau de protéines</term>
<term>Animaux</term>
<term>Humains</term>
<term>Immunoprécipitation de la chromatine</term>
<term>Modèles biologiques</term>
<term>Oligonucléotides</term>
<term>Sites de fixation</term>
<term>Souris</term>
<term>Séquençage nucléotidique à haut débit</term>
<term>Technique SELEX</term>
<term>Éléments de régulation transcriptionnelle</term>
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<front><div type="abstract" xml:lang="en"><p>Understanding gene regulation is a key challenge in today's biology. The new technologies of protein-binding microarrays (PBMs) and high-throughput SELEX (HT-SELEX) allow measurement of the binding intensities of one transcription factor (TF) to numerous synthetic double-stranded DNA sequences in a single experiment. Recently, Jolma <italic>et al.</italic>
reported the results of 547 HT-SELEX experiments covering human and mouse TFs. Because 162 of these TFs were also covered by PBM technology, for the first time, a large-scale comparison between implementations of these two <italic>in vitro</italic>
technologies is possible. Here we assessed the similarities and differences between binding models, represented as position weight matrices, inferred from PBM and HT-SELEX, and also measured how well these models predict <italic>in vivo</italic>
binding. Our results show that HT-SELEX- and PBM-derived models agree for most TFs. For some TFs, the HT-SELEX-derived models are longer versions of the PBM-derived models, whereas for other TFs, the HT-SELEX models match the secondary PBM-derived models. Remarkably, PBM-based 8-mer ranking is more accurate than that of HT-SELEX, but models derived from HT-SELEX predict <italic>in vivo</italic>
binding better. In addition, we reveal several biases in HT-SELEX data including nucleotide frequency bias, enrichment of C-rich k-mers and oligos and underrepresentation of palindromes.</p>
</div>
</front>
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