A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data
Identifieur interne : 001D62 ( Main/Exploration ); précédent : 001D61; suivant : 001D63A 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
Affiliations:
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type="wicri:Area/Main/Curation">001D62</idno><idno type="wicri:Area/Main/Exploration">001D62</idno></publicationStmt><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></author><author><name sortKey="Shamir, Ron" sort="Shamir, Ron" uniqKey="Shamir R" first="Ron" last="Shamir">Ron Shamir</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="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><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></keywords></textClass></profileDesc></teiHeader><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><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Aparicio, O" uniqKey="Aparicio O">O Aparicio</name></author><author><name sortKey="Geisberg, Jv" uniqKey="Geisberg J">JV Geisberg</name></author><author><name sortKey="Struhl, K" uniqKey="Struhl K">K Struhl</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Johnson, Ds" uniqKey="Johnson D">DS Johnson</name></author><author><name sortKey="Mortazavi, A" uniqKey="Mortazavi A">A Mortazavi</name></author><author><name sortKey="Myers, Rm" uniqKey="Myers R">RM Myers</name></author><author><name sortKey="Wold, B" uniqKey="Wold B">B Wold</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Rhee, Hs" uniqKey="Rhee H">HS Rhee</name></author><author><name 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uniqKey="Afek A">A Afek</name></author><author><name sortKey="Lukatsky, Db" uniqKey="Lukatsky D">DB Lukatsky</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Klug, Sj" uniqKey="Klug S">SJ Klug</name></author><author><name sortKey="Famulok, M" uniqKey="Famulok M">M Famulok</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Gordan, R" uniqKey="Gordan R">R Gordan</name></author><author><name sortKey="Shen, N" uniqKey="Shen N">N Shen</name></author><author><name sortKey="Dror, I" uniqKey="Dror I">I Dror</name></author><author><name sortKey="Zhou, T" uniqKey="Zhou T">T Zhou</name></author><author><name sortKey="Horton, J" uniqKey="Horton J">J Horton</name></author><author><name sortKey="Rohs, R" uniqKey="Rohs R">R Rohs</name></author><author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Yang, L" uniqKey="Yang L">L Yang</name></author><author><name sortKey="Zhou, T" uniqKey="Zhou T">T Zhou</name></author><author><name sortKey="Dror, I" uniqKey="Dror I">I Dror</name></author><author><name sortKey="Mathelier, A" uniqKey="Mathelier A">A Mathelier</name></author><author><name sortKey="Wasserman, Ww" uniqKey="Wasserman W">WW Wasserman</name></author><author><name sortKey="Gordan, R" uniqKey="Gordan R">R Gordan</name></author><author><name sortKey="Rohs, R" uniqKey="Rohs R">R Rohs</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list></list><tree><noCountry><name sortKey="Orenstein, Yaron" sort="Orenstein, Yaron" uniqKey="Orenstein Y" first="Yaron" last="Orenstein">Yaron Orenstein</name><name sortKey="Shamir, Ron" sort="Shamir, Ron" uniqKey="Shamir R" first="Ron" last="Shamir">Ron Shamir</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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