A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data
Identifieur interne : 000C79 ( Ncbi/Merge ); 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>
<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 sortKey="Pugh, Bf" uniqKey="Pugh B">BF Pugh</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name>
</author>
<author><name sortKey="Philippakis, Aa" uniqKey="Philippakis A">AA Philippakis</name>
</author>
<author><name sortKey="Qureshi, Am" uniqKey="Qureshi A">AM Qureshi</name>
</author>
<author><name sortKey="He, Fs" uniqKey="He F">FS He</name>
</author>
<author><name sortKey="Estep, Pw" uniqKey="Estep P">PW Estep</name>
</author>
<author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Fordyce, Pm" uniqKey="Fordyce P">PM Fordyce</name>
</author>
<author><name sortKey="Gerber, D" uniqKey="Gerber D">D Gerber</name>
</author>
<author><name sortKey="Tran, D" uniqKey="Tran D">D Tran</name>
</author>
<author><name sortKey="Zheng, J" uniqKey="Zheng J">J Zheng</name>
</author>
<author><name sortKey="Li, H" uniqKey="Li H">H Li</name>
</author>
<author><name sortKey="Derisi, Jl" uniqKey="Derisi J">JL DeRisi</name>
</author>
<author><name sortKey="Quake, Sr" uniqKey="Quake S">SR Quake</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jolma, A" uniqKey="Jolma A">A Jolma</name>
</author>
<author><name sortKey="Kivioja, T" uniqKey="Kivioja T">T Kivioja</name>
</author>
<author><name sortKey="Toivonen, J" uniqKey="Toivonen J">J Toivonen</name>
</author>
<author><name sortKey="Cheng, L" uniqKey="Cheng L">L Cheng</name>
</author>
<author><name sortKey="Wei, G" uniqKey="Wei G">G Wei</name>
</author>
<author><name sortKey="Enge, M" uniqKey="Enge M">M Enge</name>
</author>
<author><name sortKey="Taipale, M" uniqKey="Taipale M">M Taipale</name>
</author>
<author><name sortKey="Vaquerizas, Jm" uniqKey="Vaquerizas J">JM Vaquerizas</name>
</author>
<author><name sortKey="Yan, J" uniqKey="Yan J">J Yan</name>
</author>
<author><name sortKey="Sillanpaa, Mj" uniqKey="Sillanpaa M">MJ Sillanpaa</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Slattery, M" uniqKey="Slattery M">M Slattery</name>
</author>
<author><name sortKey="Riley, T" uniqKey="Riley T">T Riley</name>
</author>
<author><name sortKey="Liu, P" uniqKey="Liu P">P Liu</name>
</author>
<author><name sortKey="Abe, N" uniqKey="Abe N">N Abe</name>
</author>
<author><name sortKey="Gomez Alcala, P" uniqKey="Gomez Alcala P">P Gomez-Alcala</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="Rohs, R" uniqKey="Rohs R">R Rohs</name>
</author>
<author><name sortKey="Honig, B" uniqKey="Honig B">B Honig</name>
</author>
<author><name sortKey="Bussemaker, Hj" uniqKey="Bussemaker H">HJ Bussemaker</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name>
</author>
<author><name sortKey="Granas, D" uniqKey="Granas D">D Granas</name>
</author>
<author><name sortKey="Stormo, Gd" uniqKey="Stormo G">GD Stormo</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Robasky, K" uniqKey="Robasky K">K Robasky</name>
</author>
<author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Orenstein, Y" uniqKey="Orenstein Y">Y Orenstein</name>
</author>
<author><name sortKey="Linhart, C" uniqKey="Linhart C">C Linhart</name>
</author>
<author><name sortKey="Shamir, R" uniqKey="Shamir R">R Shamir</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Weirauch, Mt" uniqKey="Weirauch M">MT Weirauch</name>
</author>
<author><name sortKey="Cote, A" uniqKey="Cote A">A Cote</name>
</author>
<author><name sortKey="Norel, R" uniqKey="Norel R">R Norel</name>
</author>
<author><name sortKey="Annala, M" uniqKey="Annala M">M Annala</name>
</author>
<author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name>
</author>
<author><name sortKey="Riley, Tr" uniqKey="Riley T">TR Riley</name>
</author>
<author><name sortKey="Saez Rodriguez, J" uniqKey="Saez Rodriguez J">J Saez-Rodriguez</name>
</author>
<author><name sortKey="Cokelaer, T" uniqKey="Cokelaer T">T Cokelaer</name>
</author>
<author><name sortKey="Vedenko, A" uniqKey="Vedenko A">A Vedenko</name>
</author>
<author><name sortKey="Talukder, S" uniqKey="Talukder S">S Talukder</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jolma, A" uniqKey="Jolma A">A Jolma</name>
</author>
<author><name sortKey="Yan, J" uniqKey="Yan J">J Yan</name>
</author>
<author><name sortKey="Whitington, T" uniqKey="Whitington T">T Whitington</name>
</author>
<author><name sortKey="Toivonen, J" uniqKey="Toivonen J">J Toivonen</name>
</author>
<author><name sortKey="Nitta, Kr" uniqKey="Nitta K">KR Nitta</name>
</author>
<author><name sortKey="Rastas, P" uniqKey="Rastas P">P Rastas</name>
</author>
<author><name sortKey="Morgunova, E" uniqKey="Morgunova E">E Morgunova</name>
</author>
<author><name sortKey="Enge, M" uniqKey="Enge M">M Enge</name>
</author>
<author><name sortKey="Taipale, M" uniqKey="Taipale M">M Taipale</name>
</author>
<author><name sortKey="Wei, G" uniqKey="Wei G">G Wei</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Landt, Sg" uniqKey="Landt S">SG Landt</name>
</author>
<author><name sortKey="Marinov, Gk" uniqKey="Marinov G">GK Marinov</name>
</author>
<author><name sortKey="Kundaje, A" uniqKey="Kundaje A">A Kundaje</name>
</author>
<author><name sortKey="Kheradpour, P" uniqKey="Kheradpour P">P Kheradpour</name>
</author>
<author><name sortKey="Pauli, F" uniqKey="Pauli F">F Pauli</name>
</author>
<author><name sortKey="Batzoglou, S" uniqKey="Batzoglou S">S Batzoglou</name>
</author>
<author><name sortKey="Bernstein, Be" uniqKey="Bernstein B">BE Bernstein</name>
</author>
<author><name sortKey="Bickel, P" uniqKey="Bickel P">P Bickel</name>
</author>
<author><name sortKey="Brown, Jb" uniqKey="Brown J">JB Brown</name>
</author>
<author><name sortKey="Cayting, P" uniqKey="Cayting P">P Cayting</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stormo, Gd" uniqKey="Stormo G">GD Stormo</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chen, X" uniqKey="Chen X">X Chen</name>
</author>
<author><name sortKey="Hughes, Tr" uniqKey="Hughes T">TR Hughes</name>
</author>
<author><name sortKey="Morris, Q" uniqKey="Morris Q">Q Morris</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Badis, G" uniqKey="Badis G">G Badis</name>
</author>
<author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name>
</author>
<author><name sortKey="Philippakis, Aa" uniqKey="Philippakis A">AA Philippakis</name>
</author>
<author><name sortKey="Talukder, S" uniqKey="Talukder S">S Talukder</name>
</author>
<author><name sortKey="Gehrke, Ar" uniqKey="Gehrke A">AR Gehrke</name>
</author>
<author><name sortKey="Jaeger, Sa" uniqKey="Jaeger S">SA Jaeger</name>
</author>
<author><name sortKey="Chan, Et" uniqKey="Chan E">ET Chan</name>
</author>
<author><name sortKey="Metzler, G" uniqKey="Metzler G">G Metzler</name>
</author>
<author><name sortKey="Vedenko, A" uniqKey="Vedenko A">A Vedenko</name>
</author>
<author><name sortKey="Chen, X" uniqKey="Chen X">X Chen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name>
</author>
<author><name sortKey="Stormo, Gd" uniqKey="Stormo G">GD Stormo</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Orenstein, Y" uniqKey="Orenstein Y">Y Orenstein</name>
</author>
<author><name sortKey="Mick, E" uniqKey="Mick E">E Mick</name>
</author>
<author><name sortKey="Shamir, R" uniqKey="Shamir R">R Shamir</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name>
</author>
<author><name sortKey="Badis, G" uniqKey="Badis G">G Badis</name>
</author>
<author><name sortKey="Gehrke, Ar" uniqKey="Gehrke A">AR Gehrke</name>
</author>
<author><name sortKey="Talukder, S" uniqKey="Talukder S">S Talukder</name>
</author>
<author><name sortKey="Philippakis, Aa" uniqKey="Philippakis A">AA Philippakis</name>
</author>
<author><name sortKey="Pena Castillo, L" uniqKey="Pena Castillo L">L Pena-Castillo</name>
</author>
<author><name sortKey="Alleyne, Tm" uniqKey="Alleyne T">TM Alleyne</name>
</author>
<author><name sortKey="Mnaimneh, S" uniqKey="Mnaimneh S">S Mnaimneh</name>
</author>
<author><name sortKey="Botvinnik, Ob" uniqKey="Botvinnik O">OB Botvinnik</name>
</author>
<author><name sortKey="Chan, Et" uniqKey="Chan E">ET Chan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wei, Gh" uniqKey="Wei G">GH Wei</name>
</author>
<author><name sortKey="Badis, G" uniqKey="Badis G">G Badis</name>
</author>
<author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name>
</author>
<author><name sortKey="Kivioja, T" uniqKey="Kivioja T">T Kivioja</name>
</author>
<author><name sortKey="Palin, K" uniqKey="Palin K">K Palin</name>
</author>
<author><name sortKey="Enge, M" uniqKey="Enge M">M Enge</name>
</author>
<author><name sortKey="Bonke, M" uniqKey="Bonke M">M Bonke</name>
</author>
<author><name sortKey="Jolma, A" uniqKey="Jolma A">A Jolma</name>
</author>
<author><name sortKey="Varjosalo, M" uniqKey="Varjosalo M">M Varjosalo</name>
</author>
<author><name sortKey="Gehrke, Ar" uniqKey="Gehrke A">AR Gehrke</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rohs, R" uniqKey="Rohs R">R Rohs</name>
</author>
<author><name sortKey="Jin, X" uniqKey="Jin X">X Jin</name>
</author>
<author><name sortKey="West, Sm" uniqKey="West S">SM West</name>
</author>
<author><name sortKey="Joshi, R" uniqKey="Joshi R">R Joshi</name>
</author>
<author><name sortKey="Honig, B" uniqKey="Honig B">B Honig</name>
</author>
<author><name sortKey="Mann, Rs" uniqKey="Mann R">RS Mann</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bailey, Tl" uniqKey="Bailey T">TL Bailey</name>
</author>
<author><name sortKey="Machanick, P" uniqKey="Machanick P">P Machanick</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Park, Pj" uniqKey="Park P">PJ Park</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Aird, D" uniqKey="Aird D">D Aird</name>
</author>
<author><name sortKey="Ross, Mg" uniqKey="Ross M">MG Ross</name>
</author>
<author><name sortKey="Chen, Ws" uniqKey="Chen W">WS Chen</name>
</author>
<author><name sortKey="Danielsson, M" uniqKey="Danielsson M">M Danielsson</name>
</author>
<author><name sortKey="Fennell, T" uniqKey="Fennell T">T Fennell</name>
</author>
<author><name sortKey="Russ, C" uniqKey="Russ C">C Russ</name>
</author>
<author><name sortKey="Jaffe, Db" uniqKey="Jaffe D">DB Jaffe</name>
</author>
<author><name sortKey="Nusbaum, C" uniqKey="Nusbaum C">C Nusbaum</name>
</author>
<author><name sortKey="Gnirke, A" uniqKey="Gnirke A">A Gnirke</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hansen, Kd" uniqKey="Hansen K">KD Hansen</name>
</author>
<author><name sortKey="Brenner, Se" uniqKey="Brenner S">SE Brenner</name>
</author>
<author><name sortKey="Dudoit, S" uniqKey="Dudoit S">S Dudoit</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Barski, A" uniqKey="Barski A">A Barski</name>
</author>
<author><name sortKey="Zhao, K" uniqKey="Zhao K">K Zhao</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jiang, B" uniqKey="Jiang B">B Jiang</name>
</author>
<author><name sortKey="Liu, Js" uniqKey="Liu J">JS Liu</name>
</author>
<author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Afek, A" 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>
<double pmid="24500199"><pmc><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">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>
</titleStmt>
<publicationStmt><idno type="wicri:source">PMC</idno>
<idno type="pmid">24500199</idno>
<idno type="pmc">4005680</idno>
<idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4005680</idno>
<idno type="RBID">PMC:4005680</idno>
<idno type="doi">10.1093/nar/gku117</idno>
<date when="2014">2014</date>
<idno type="wicri:Area/Pmc/Corpus">000F54</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000F54</idno>
<idno type="wicri:Area/Pmc/Curation">000F54</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000F54</idno>
<idno type="wicri:Area/Pmc/Checkpoint">001145</idno>
<idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001145</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></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 sortKey="Pugh, Bf" uniqKey="Pugh B">BF Pugh</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name>
</author>
<author><name sortKey="Philippakis, Aa" uniqKey="Philippakis A">AA Philippakis</name>
</author>
<author><name sortKey="Qureshi, Am" uniqKey="Qureshi A">AM Qureshi</name>
</author>
<author><name sortKey="He, Fs" uniqKey="He F">FS He</name>
</author>
<author><name sortKey="Estep, Pw" uniqKey="Estep P">PW Estep</name>
</author>
<author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Fordyce, Pm" uniqKey="Fordyce P">PM Fordyce</name>
</author>
<author><name sortKey="Gerber, D" uniqKey="Gerber D">D Gerber</name>
</author>
<author><name sortKey="Tran, D" uniqKey="Tran D">D Tran</name>
</author>
<author><name sortKey="Zheng, J" uniqKey="Zheng J">J Zheng</name>
</author>
<author><name sortKey="Li, H" uniqKey="Li H">H Li</name>
</author>
<author><name sortKey="Derisi, Jl" uniqKey="Derisi J">JL DeRisi</name>
</author>
<author><name sortKey="Quake, Sr" uniqKey="Quake S">SR Quake</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jolma, A" uniqKey="Jolma A">A Jolma</name>
</author>
<author><name sortKey="Kivioja, T" uniqKey="Kivioja T">T Kivioja</name>
</author>
<author><name sortKey="Toivonen, J" uniqKey="Toivonen J">J Toivonen</name>
</author>
<author><name sortKey="Cheng, L" uniqKey="Cheng L">L Cheng</name>
</author>
<author><name sortKey="Wei, G" uniqKey="Wei G">G Wei</name>
</author>
<author><name sortKey="Enge, M" uniqKey="Enge M">M Enge</name>
</author>
<author><name sortKey="Taipale, M" uniqKey="Taipale M">M Taipale</name>
</author>
<author><name sortKey="Vaquerizas, Jm" uniqKey="Vaquerizas J">JM Vaquerizas</name>
</author>
<author><name sortKey="Yan, J" uniqKey="Yan J">J Yan</name>
</author>
<author><name sortKey="Sillanpaa, Mj" uniqKey="Sillanpaa M">MJ Sillanpaa</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Slattery, M" uniqKey="Slattery M">M Slattery</name>
</author>
<author><name sortKey="Riley, T" uniqKey="Riley T">T Riley</name>
</author>
<author><name sortKey="Liu, P" uniqKey="Liu P">P Liu</name>
</author>
<author><name sortKey="Abe, N" uniqKey="Abe N">N Abe</name>
</author>
<author><name sortKey="Gomez Alcala, P" uniqKey="Gomez Alcala P">P Gomez-Alcala</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="Rohs, R" uniqKey="Rohs R">R Rohs</name>
</author>
<author><name sortKey="Honig, B" uniqKey="Honig B">B Honig</name>
</author>
<author><name sortKey="Bussemaker, Hj" uniqKey="Bussemaker H">HJ Bussemaker</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name>
</author>
<author><name sortKey="Granas, D" uniqKey="Granas D">D Granas</name>
</author>
<author><name sortKey="Stormo, Gd" uniqKey="Stormo G">GD Stormo</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Robasky, K" uniqKey="Robasky K">K Robasky</name>
</author>
<author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Orenstein, Y" uniqKey="Orenstein Y">Y Orenstein</name>
</author>
<author><name sortKey="Linhart, C" uniqKey="Linhart C">C Linhart</name>
</author>
<author><name sortKey="Shamir, R" uniqKey="Shamir R">R Shamir</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Weirauch, Mt" uniqKey="Weirauch M">MT Weirauch</name>
</author>
<author><name sortKey="Cote, A" uniqKey="Cote A">A Cote</name>
</author>
<author><name sortKey="Norel, R" uniqKey="Norel R">R Norel</name>
</author>
<author><name sortKey="Annala, M" uniqKey="Annala M">M Annala</name>
</author>
<author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name>
</author>
<author><name sortKey="Riley, Tr" uniqKey="Riley T">TR Riley</name>
</author>
<author><name sortKey="Saez Rodriguez, J" uniqKey="Saez Rodriguez J">J Saez-Rodriguez</name>
</author>
<author><name sortKey="Cokelaer, T" uniqKey="Cokelaer T">T Cokelaer</name>
</author>
<author><name sortKey="Vedenko, A" uniqKey="Vedenko A">A Vedenko</name>
</author>
<author><name sortKey="Talukder, S" uniqKey="Talukder S">S Talukder</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jolma, A" uniqKey="Jolma A">A Jolma</name>
</author>
<author><name sortKey="Yan, J" uniqKey="Yan J">J Yan</name>
</author>
<author><name sortKey="Whitington, T" uniqKey="Whitington T">T Whitington</name>
</author>
<author><name sortKey="Toivonen, J" uniqKey="Toivonen J">J Toivonen</name>
</author>
<author><name sortKey="Nitta, Kr" uniqKey="Nitta K">KR Nitta</name>
</author>
<author><name sortKey="Rastas, P" uniqKey="Rastas P">P Rastas</name>
</author>
<author><name sortKey="Morgunova, E" uniqKey="Morgunova E">E Morgunova</name>
</author>
<author><name sortKey="Enge, M" uniqKey="Enge M">M Enge</name>
</author>
<author><name sortKey="Taipale, M" uniqKey="Taipale M">M Taipale</name>
</author>
<author><name sortKey="Wei, G" uniqKey="Wei G">G Wei</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Landt, Sg" uniqKey="Landt S">SG Landt</name>
</author>
<author><name sortKey="Marinov, Gk" uniqKey="Marinov G">GK Marinov</name>
</author>
<author><name sortKey="Kundaje, A" uniqKey="Kundaje A">A Kundaje</name>
</author>
<author><name sortKey="Kheradpour, P" uniqKey="Kheradpour P">P Kheradpour</name>
</author>
<author><name sortKey="Pauli, F" uniqKey="Pauli F">F Pauli</name>
</author>
<author><name sortKey="Batzoglou, S" uniqKey="Batzoglou S">S Batzoglou</name>
</author>
<author><name sortKey="Bernstein, Be" uniqKey="Bernstein B">BE Bernstein</name>
</author>
<author><name sortKey="Bickel, P" uniqKey="Bickel P">P Bickel</name>
</author>
<author><name sortKey="Brown, Jb" uniqKey="Brown J">JB Brown</name>
</author>
<author><name sortKey="Cayting, P" uniqKey="Cayting P">P Cayting</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Stormo, Gd" uniqKey="Stormo G">GD Stormo</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Chen, X" uniqKey="Chen X">X Chen</name>
</author>
<author><name sortKey="Hughes, Tr" uniqKey="Hughes T">TR Hughes</name>
</author>
<author><name sortKey="Morris, Q" uniqKey="Morris Q">Q Morris</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Badis, G" uniqKey="Badis G">G Badis</name>
</author>
<author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name>
</author>
<author><name sortKey="Philippakis, Aa" uniqKey="Philippakis A">AA Philippakis</name>
</author>
<author><name sortKey="Talukder, S" uniqKey="Talukder S">S Talukder</name>
</author>
<author><name sortKey="Gehrke, Ar" uniqKey="Gehrke A">AR Gehrke</name>
</author>
<author><name sortKey="Jaeger, Sa" uniqKey="Jaeger S">SA Jaeger</name>
</author>
<author><name sortKey="Chan, Et" uniqKey="Chan E">ET Chan</name>
</author>
<author><name sortKey="Metzler, G" uniqKey="Metzler G">G Metzler</name>
</author>
<author><name sortKey="Vedenko, A" uniqKey="Vedenko A">A Vedenko</name>
</author>
<author><name sortKey="Chen, X" uniqKey="Chen X">X Chen</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name>
</author>
<author><name sortKey="Stormo, Gd" uniqKey="Stormo G">GD Stormo</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Orenstein, Y" uniqKey="Orenstein Y">Y Orenstein</name>
</author>
<author><name sortKey="Mick, E" uniqKey="Mick E">E Mick</name>
</author>
<author><name sortKey="Shamir, R" uniqKey="Shamir R">R Shamir</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name>
</author>
<author><name sortKey="Badis, G" uniqKey="Badis G">G Badis</name>
</author>
<author><name sortKey="Gehrke, Ar" uniqKey="Gehrke A">AR Gehrke</name>
</author>
<author><name sortKey="Talukder, S" uniqKey="Talukder S">S Talukder</name>
</author>
<author><name sortKey="Philippakis, Aa" uniqKey="Philippakis A">AA Philippakis</name>
</author>
<author><name sortKey="Pena Castillo, L" uniqKey="Pena Castillo L">L Pena-Castillo</name>
</author>
<author><name sortKey="Alleyne, Tm" uniqKey="Alleyne T">TM Alleyne</name>
</author>
<author><name sortKey="Mnaimneh, S" uniqKey="Mnaimneh S">S Mnaimneh</name>
</author>
<author><name sortKey="Botvinnik, Ob" uniqKey="Botvinnik O">OB Botvinnik</name>
</author>
<author><name sortKey="Chan, Et" uniqKey="Chan E">ET Chan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Wei, Gh" uniqKey="Wei G">GH Wei</name>
</author>
<author><name sortKey="Badis, G" uniqKey="Badis G">G Badis</name>
</author>
<author><name sortKey="Berger, Mf" uniqKey="Berger M">MF Berger</name>
</author>
<author><name sortKey="Kivioja, T" uniqKey="Kivioja T">T Kivioja</name>
</author>
<author><name sortKey="Palin, K" uniqKey="Palin K">K Palin</name>
</author>
<author><name sortKey="Enge, M" uniqKey="Enge M">M Enge</name>
</author>
<author><name sortKey="Bonke, M" uniqKey="Bonke M">M Bonke</name>
</author>
<author><name sortKey="Jolma, A" uniqKey="Jolma A">A Jolma</name>
</author>
<author><name sortKey="Varjosalo, M" uniqKey="Varjosalo M">M Varjosalo</name>
</author>
<author><name sortKey="Gehrke, Ar" uniqKey="Gehrke A">AR Gehrke</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Rohs, R" uniqKey="Rohs R">R Rohs</name>
</author>
<author><name sortKey="Jin, X" uniqKey="Jin X">X Jin</name>
</author>
<author><name sortKey="West, Sm" uniqKey="West S">SM West</name>
</author>
<author><name sortKey="Joshi, R" uniqKey="Joshi R">R Joshi</name>
</author>
<author><name sortKey="Honig, B" uniqKey="Honig B">B Honig</name>
</author>
<author><name sortKey="Mann, Rs" uniqKey="Mann R">RS Mann</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bailey, Tl" uniqKey="Bailey T">TL Bailey</name>
</author>
<author><name sortKey="Machanick, P" uniqKey="Machanick P">P Machanick</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Park, Pj" uniqKey="Park P">PJ Park</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Aird, D" uniqKey="Aird D">D Aird</name>
</author>
<author><name sortKey="Ross, Mg" uniqKey="Ross M">MG Ross</name>
</author>
<author><name sortKey="Chen, Ws" uniqKey="Chen W">WS Chen</name>
</author>
<author><name sortKey="Danielsson, M" uniqKey="Danielsson M">M Danielsson</name>
</author>
<author><name sortKey="Fennell, T" uniqKey="Fennell T">T Fennell</name>
</author>
<author><name sortKey="Russ, C" uniqKey="Russ C">C Russ</name>
</author>
<author><name sortKey="Jaffe, Db" uniqKey="Jaffe D">DB Jaffe</name>
</author>
<author><name sortKey="Nusbaum, C" uniqKey="Nusbaum C">C Nusbaum</name>
</author>
<author><name sortKey="Gnirke, A" uniqKey="Gnirke A">A Gnirke</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Hansen, Kd" uniqKey="Hansen K">KD Hansen</name>
</author>
<author><name sortKey="Brenner, Se" uniqKey="Brenner S">SE Brenner</name>
</author>
<author><name sortKey="Dudoit, S" uniqKey="Dudoit S">S Dudoit</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Barski, A" uniqKey="Barski A">A Barski</name>
</author>
<author><name sortKey="Zhao, K" uniqKey="Zhao K">K Zhao</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jiang, B" uniqKey="Jiang B">B Jiang</name>
</author>
<author><name sortKey="Liu, Js" uniqKey="Liu J">JS Liu</name>
</author>
<author><name sortKey="Bulyk, Ml" uniqKey="Bulyk M">ML Bulyk</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Afek, A" 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>
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</author>
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</author>
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<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>
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</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>
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<pubmed><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">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>
<affiliation wicri:level="1"><nlm:affiliation>Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv 69978, Israel.</nlm:affiliation>
<country xml:lang="fr">Israël</country>
<wicri:regionArea>Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv 69978</wicri:regionArea>
<wicri:noRegion>Tel Aviv 69978</wicri:noRegion>
</affiliation>
</author>
<author><name sortKey="Shamir, Ron" sort="Shamir, Ron" uniqKey="Shamir R" first="Ron" last="Shamir">Ron Shamir</name>
</author>
</titleStmt>
<publicationStmt><idno type="wicri:source">PubMed</idno>
<date when="2014">2014</date>
<idno type="RBID">pubmed:24500199</idno>
<idno type="pmid">24500199</idno>
<idno type="doi">10.1093/nar/gku117</idno>
<idno type="wicri:Area/PubMed/Corpus">001A64</idno>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">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>
<affiliation wicri:level="1"><nlm:affiliation>Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv 69978, Israel.</nlm:affiliation>
<country xml:lang="fr">Israël</country>
<wicri:regionArea>Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv 69978</wicri:regionArea>
<wicri:noRegion>Tel Aviv 69978</wicri:noRegion>
</affiliation>
</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="eISSN">1362-4962</idno>
<imprint><date when="2014" type="published">2014</date>
</imprint>
</series>
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</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">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 et al. 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 in vitro 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 in vivo 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 in vivo 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. </div>
</front>
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