A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data
Identifieur interne : 001145 ( Pmc/Checkpoint ); précédent : 001144; suivant : 001146A 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.
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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<record><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>
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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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<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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<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>
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<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>
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<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id>
<journal-id journal-id-type="iso-abbrev">Nucleic Acids Res</journal-id>
<journal-id journal-id-type="publisher-id">nar</journal-id>
<journal-id journal-id-type="hwp">nar</journal-id>
<journal-title-group><journal-title>Nucleic Acids Research</journal-title>
</journal-title-group>
<issn pub-type="ppub">0305-1048</issn>
<issn pub-type="epub">1362-4962</issn>
<publisher><publisher-name>Oxford University Press</publisher-name>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">24500199</article-id>
<article-id pub-id-type="pmc">4005680</article-id>
<article-id pub-id-type="doi">10.1093/nar/gku117</article-id>
<article-id pub-id-type="publisher-id">gku117</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Methods Online</subject>
</subj-group>
</article-categories>
<title-group><article-title>A comparative analysis of transcription factor binding models learned from PBM, HT-SELEX and ChIP data</article-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Orenstein</surname>
<given-names>Yaron</given-names>
</name>
</contrib>
<contrib contrib-type="author"><name><surname>Shamir</surname>
<given-names>Ron</given-names>
</name>
<xref ref-type="corresp" rid="gku117-COR1">*</xref>
</contrib>
<aff>Blavatnik School of Computer Science, Tel-Aviv University, Tel Aviv 69978, Israel</aff>
</contrib-group>
<author-notes><corresp id="gku117-COR1">*To whom correspondence should be addressed. Tel: <phone>+972 3 6405383</phone>
; Fax: <fax>+972 3 640 5384</fax>
; Email: <email>rshamir@tau.ac.il</email>
</corresp>
<fn><p>Present address: Ron Shamir, School of Computer Science, Tel-Aviv University, P.O.B. 39040, Tel-Aviv 69978, Israel.</p>
</fn>
</author-notes>
<pub-date pub-type="ppub"><month>4</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="epub"><day>5</day>
<month>2</month>
<year>2014</year>
</pub-date>
<pub-date pub-type="pmc-release"><day>5</day>
<month>2</month>
<year>2014</year>
</pub-date>
<pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
. </pmc-comment>
<volume>42</volume>
<issue>8</issue>
<fpage>e63</fpage>
<lpage>e63</lpage>
<history><date date-type="received"><day>11</day>
<month>11</month>
<year>2013</year>
</date>
<date date-type="rev-recd"><day>22</day>
<month>12</month>
<year>2013</year>
</date>
<date date-type="accepted"><day>16</day>
<month>1</month>
<year>2014</year>
</date>
</history>
<permissions><copyright-statement>© The Author(s) 2014. Published by Oxford University Press.</copyright-statement>
<copyright-year>2014</copyright-year>
<license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by/3.0/"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/3.0/">http://creativecommons.org/licenses/by/3.0/</ext-link>
), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p>
</license>
</permissions>
<abstract><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>
</abstract>
<counts><page-count count="10"></page-count>
</counts>
</article-meta>
</front>
</pmc>
<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>
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