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Volumn 91, Issue , 2013, Pages 135-171

DNA sequence motif: A jack of all trades for Chip-Seq data

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DNA;

EID: 84879332802     PISSN: 18761623     EISSN: None     Source Type: Book Series    
DOI: 10.1016/B978-0-12-411637-5.00005-6     Document Type: Chapter
Times cited : (12)

References (117)
  • 1
    • 84867399412 scopus 로고    scopus 로고
    • MKNK1 is a YB-1 target gene responsible for imparting trastuzumab resistance and can be blocked by RSK inhibition
    • A. Astanehe, M.R. Finkbeiner, M. Krzywinski, A. Fotovati, J. Dhillon, and I.M. Berquin MKNK1 is a YB-1 target gene responsible for imparting trastuzumab resistance and can be blocked by RSK inhibition Oncogene 31 41 2012 4434 4446
    • (2012) Oncogene , vol.31 , Issue.41 , pp. 4434-4446
    • Astanehe, A.1    Finkbeiner, M.R.2    Krzywinski, M.3    Fotovati, A.4    Dhillon, J.5    Berquin, I.M.6
  • 5
    • 84866937220 scopus 로고    scopus 로고
    • Inferring direct DNA binding from ChIP-seq
    • T.L. Bailey, and P. Machanick Inferring direct DNA binding from ChIP-seq Nucleic Acids Research 40 17 2012 e128
    • (2012) Nucleic Acids Research , vol.40 , Issue.17 , pp. 128
    • Bailey, T.L.1    Machanick, P.2
  • 6
    • 0037109192 scopus 로고    scopus 로고
    • Additivity in protein-DNA interactions: How good an approximation is it?
    • P.V. Benos, M.L. Bulyk, and G.D. Stormo Additivity in protein-DNA interactions: How good an approximation is it? Nucleic Acids Research 30 20 2002 4442 4451
    • (2002) Nucleic Acids Research , vol.30 , Issue.20 , pp. 4442-4451
    • Benos, P.V.1    Bulyk, M.L.2    Stormo, G.D.3
  • 7
    • 0023147228 scopus 로고
    • Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters
    • O.G. Berg, and P.H. von Hippel Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters Journal of Molecular Biology 193 4 1987 723 750
    • (1987) Journal of Molecular Biology , vol.193 , Issue.4 , pp. 723-750
    • Berg, O.G.1    Von Hippel, P.H.2
  • 8
    • 0023947427 scopus 로고
    • Selection of DNA binding sites by regulatory proteins
    • O.G. Berg, and P.H. von Hippel Selection of DNA binding sites by regulatory proteins Trends in Biochemical Sciences 13 6 1988 207 211
    • (1988) Trends in Biochemical Sciences , vol.13 , Issue.6 , pp. 207-211
    • Berg, O.G.1    Von Hippel, P.H.2
  • 9
    • 80052401846 scopus 로고    scopus 로고
    • Tree-based position weight matrix approach to model transcription factor binding site profiles
    • Y. Bi, H. Kim, R. Gupta, and R.V. Davuluri Tree-based position weight matrix approach to model transcription factor binding site profiles PLoS One 6 9 2011 e24210
    • (2011) PLoS One , vol.6 , Issue.9 , pp. 24210
    • Bi, Y.1    Kim, H.2    Gupta, R.3    Davuluri, R.V.4
  • 10
    • 77951230100 scopus 로고    scopus 로고
    • Sole-Search: An integrated analysis program for peak detection and functional annotation using ChIP-seq data
    • K.R. Blahnik, L. Dou, H. O'Geen, T. McPhillips, X. Xu, and A.R. Cao Sole-Search: An integrated analysis program for peak detection and functional annotation using ChIP-seq data Nucleic Acids Research 38 3 2010 e13
    • (2010) Nucleic Acids Research , vol.38 , Issue.3 , pp. 13
    • Blahnik, K.R.1    Dou, L.2    O'Geen, H.3    McPhillips, T.4    Xu, X.5    Cao, A.R.6
  • 12
    • 77954355124 scopus 로고    scopus 로고
    • De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis
    • V. Boeva, D. Surdez, N. Guillon, F. Tirode, A.P. Fejes, and O. Delattre De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis Nucleic Acids Research 38 11 2010 e126
    • (2010) Nucleic Acids Research , vol.38 , Issue.11 , pp. 126
    • Boeva, V.1    Surdez, D.2    Guillon, N.3    Tirode, F.4    Fejes, A.P.5    Delattre, O.6
  • 13
    • 1242316281 scopus 로고    scopus 로고
    • ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    • M.J. Buck, and J.D. Lieb ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments Genomics 83 3 2004 349 360
    • (2004) Genomics , vol.83 , Issue.3 , pp. 349-360
    • Buck, M.J.1    Lieb, J.D.2
  • 14
    • 33746829957 scopus 로고    scopus 로고
    • DNA microarray technologies for measuring protein-DNA interactions
    • M.L. Bulyk DNA microarray technologies for measuring protein-DNA interactions Current Opinion in Biotechnology 17 4 2006 422 430
    • (2006) Current Opinion in Biotechnology , vol.17 , Issue.4 , pp. 422-430
    • Bulyk, M.L.1
  • 15
    • 44649117905 scopus 로고    scopus 로고
    • Integration of external signaling pathways with the core transcriptional network in embryonic stem cells
    • X. Chen, H. Xu, P. Yuan, F. Fang, M. Huss, and V.B. Vega Integration of external signaling pathways with the core transcriptional network in embryonic stem cells Cell 133 6 2008 1106 1117
    • (2008) Cell , vol.133 , Issue.6 , pp. 1106-1117
    • Chen, X.1    Xu, H.2    Yuan, P.3    Fang, F.4    Huss, M.5    Vega, V.B.6
  • 17
    • 38549144819 scopus 로고    scopus 로고
    • A survey of DNA motif finding algorithms
    • M.K. Das, and H.-K. Dai A survey of DNA motif finding algorithms BMC Bioinformatics 8 Suppl. 7 2007 S21
    • (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 7 , pp. 21
    • Das, M.K.1    Dai, H.-K.2
  • 18
    • 0026598149 scopus 로고
    • Critical comparison of consensus methods for molecular sequences
    • W.H. Day, and F.R. McMorris Critical comparison of consensus methods for molecular sequences Nucleic Acids Research 20 5 1992 1093 1099
    • (1992) Nucleic Acids Research , vol.20 , Issue.5 , pp. 1093-1099
    • Day, W.H.1    McMorris, F.R.2
  • 19
    • 33645748095 scopus 로고    scopus 로고
    • What are DNA sequence motifs?
    • P. D'haeseleer What are DNA sequence motifs? Nature Biotechnology 24 4 2006 423 425
    • (2006) Nature Biotechnology , vol.24 , Issue.4 , pp. 423-425
    • D'Haeseleer, P.1
  • 20
    • 84883488207 scopus 로고    scopus 로고
    • YB-1 (YBX1) does not bind to Y/CCAAT boxes in vivo
    • 10.1038/onc.2012.521
    • D. Dolfini, and R. Mantovani YB-1 (YBX1) does not bind to Y/CCAAT boxes in vivo Oncogene 2012 10.1038/onc.2012.521
    • (2012) Oncogene
    • Dolfini, D.1    Mantovani, R.2
  • 21
  • 22
    • 34547662962 scopus 로고    scopus 로고
    • Trawler: De novo regulatory motif discovery pipeline for chromatin immunoprecipitation
    • L. Ettwiller, B. Paten, M. Ramialison, E. Birney, and J. Wittbrodt Trawler: De novo regulatory motif discovery pipeline for chromatin immunoprecipitation Nature Methods 4 7 2007 563 565
    • (2007) Nature Methods , vol.4 , Issue.7 , pp. 563-565
    • Ettwiller, L.1    Paten, B.2    Ramialison, M.3    Birney, E.4    Wittbrodt, J.5
  • 23
    • 19544379737 scopus 로고    scopus 로고
    • A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length
    • A.V. Favorov, M.S. Gelfand, A.V. Gerasimova, D.A. Ravcheev, A.A. Mironov, and V.J. Makeev A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length Bioinformatics 21 10 2005 2240 2245
    • (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2240-2245
    • Favorov, A.V.1    Gelfand, M.S.2    Gerasimova, A.V.3    Ravcheev, D.A.4    Mironov, A.A.5    Makeev, V.J.6
  • 24
    • 48249140621 scopus 로고    scopus 로고
    • FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology
    • A.P. Fejes, G. Robertson, M. Bilenky, R. Varhol, M. Bainbridge, and S.J.M. Jones FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology Bioinformatics (Oxford, England) 24 15 2008 1729 1730
    • (2008) Bioinformatics (Oxford, England) , vol.24 , Issue.15 , pp. 1729-1730
    • Fejes, A.P.1    Robertson, G.2    Bilenky, M.3    Varhol, R.4    Bainbridge, M.5    Jones, S.J.M.6
  • 25
    • 84866127830 scopus 로고    scopus 로고
    • Identifying ChIP-seq enrichment using MACS
    • J. Feng, T. Liu, B. Qin, Y. Zhang, and X.S. Liu Identifying ChIP-seq enrichment using MACS Nature Protocols 7 9 2012 1728 1740
    • (2012) Nature Protocols , vol.7 , Issue.9 , pp. 1728-1740
    • Feng, J.1    Liu, T.2    Qin, B.3    Zhang, Y.4    Liu, X.S.5
  • 26
    • 70449701942 scopus 로고    scopus 로고
    • Sense from sequence reads: Methods for alignment and assembly
    • P. Flicek, and E. Birney Sense from sequence reads: Methods for alignment and assembly Nature Methods 6 11 Suppl. 2009 S6 S12
    • (2009) Nature Methods , vol.6 , Issue.11 SUPPL.
    • Flicek, P.1    Birney, E.2
  • 27
    • 0018199224 scopus 로고
    • DNAse footprinting: A simple method for the detection of protein-DNA binding specificity
    • D.J. Galas, and A. Schmitz DNAse footprinting: A simple method for the detection of protein-DNA binding specificity Nucleic Acids Research 5 9 1978 3157 3170
    • (1978) Nucleic Acids Research , vol.5 , Issue.9 , pp. 3157-3170
    • Galas, D.J.1    Schmitz, A.2
  • 28
    • 17644369311 scopus 로고    scopus 로고
    • Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites
    • N.I. Gershenzon, G.D. Stormo, and I.P. Ioshikhes Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites Nucleic Acids Research 33 7 2005 2290 2301
    • (2005) Nucleic Acids Research , vol.33 , Issue.7 , pp. 2290-2301
    • Gershenzon, N.I.1    Stormo, G.D.2    Ioshikhes, I.P.3
  • 29
    • 77951874066 scopus 로고    scopus 로고
    • Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers
    • V. Gotea, A. Visel, J.M. Westlund, M.A. Nobrega, L.A. Pennacchio, and I. Ovcharenko Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers Genome Research 20 5 2010 565 577
    • (2010) Genome Research , vol.20 , Issue.5 , pp. 565-577
    • Gotea, V.1    Visel, A.2    Westlund, J.M.3    Nobrega, M.A.4    Pennacchio, L.A.5    Ovcharenko, I.6
  • 30
    • 63349090507 scopus 로고    scopus 로고
    • The oncogenic EWS-FLI1 protein binds in vivo GGAA microsatellite sequences with potential transcriptional activation function
    • N. Guillon, F. Tirode, V. Boeva, A. Zynovyev, E. Barillot, and O. Delattre The oncogenic EWS-FLI1 protein binds in vivo GGAA microsatellite sequences with potential transcriptional activation function PLoS One 4 3 2009 e4932
    • (2009) PLoS One , vol.4 , Issue.3 , pp. 4932
    • Guillon, N.1    Tirode, F.2    Boeva, V.3    Zynovyev, A.4    Barillot, E.5    Delattre, O.6
  • 31
    • 39149128313 scopus 로고    scopus 로고
    • A hybrid model for robust detection of transcription factor binding sites
    • S. Gunewardena, and Z. Zhang A hybrid model for robust detection of transcription factor binding sites Bioinformatics (Oxford, England) 24 4 2008 484 491
    • (2008) Bioinformatics (Oxford, England) , vol.24 , Issue.4 , pp. 484-491
    • Gunewardena, S.1    Zhang, Z.2
  • 32
    • 84866086842 scopus 로고    scopus 로고
    • High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints
    • Y. Guo, S. Mahony, and D.K. Gifford High resolution genome wide binding event finding and motif discovery reveals transcription factor spatial binding constraints PLoS Computational Biology 8 8 2012 e1002638
    • (2012) PLoS Computational Biology , vol.8 , Issue.8 , pp. 1002638
    • Guo, Y.1    Mahony, S.2    Gifford, D.K.3
  • 34
    • 84871261147 scopus 로고    scopus 로고
    • COPS: Detecting co-occurrence and spatial arrangement of transcription factor binding motifs in genome-wide datasets
    • N. Ha, M. Polychronidou, and I. Lohmann COPS: Detecting co-occurrence and spatial arrangement of transcription factor binding motifs in genome-wide datasets PLoS One 7 12 2012 e52055
    • (2012) PLoS One , vol.7 , Issue.12 , pp. 52055
    • Ha, N.1    Polychronidou, M.2    Lohmann, I.3
  • 35
    • 29144484156 scopus 로고    scopus 로고
    • Enhanced position weight matrices using mixture models
    • S. Hannenhalli, and L.-S. Wang Enhanced position weight matrices using mixture models Bioinformatics (Oxford, England) 21 Suppl. 1 2005 i204 i212
    • (2005) Bioinformatics (Oxford, England) , vol.21 , Issue.SUPPL. 1
    • Hannenhalli, S.1    Wang, L.-S.2
  • 37
    • 0036270889 scopus 로고    scopus 로고
    • ChIP-chip: A genomic approach for identifying transcription factor binding sites
    • C.E. Horak, and M. Snyder ChIP-chip: A genomic approach for identifying transcription factor binding sites Methods in Enzymology 350 2002 469 483
    • (2002) Methods in Enzymology , vol.350 , pp. 469-483
    • Horak, C.E.1    Snyder, M.2
  • 38
    • 77949916244 scopus 로고    scopus 로고
    • On the detection and refinement of transcription factor binding sites using ChIP-Seq data
    • M. Hu, J. Yu, J.M.G. Taylor, A.M. Chinnaiyan, and Z.S. Qin On the detection and refinement of transcription factor binding sites using ChIP-Seq data Nucleic Acids Research 38 7 2010 2154 2167
    • (2010) Nucleic Acids Research , vol.38 , Issue.7 , pp. 2154-2167
    • Hu, M.1    Yu, J.2    Taylor, J.M.G.3    Chinnaiyan, A.M.4    Qin, Z.S.5
  • 39
    • 19944367254 scopus 로고    scopus 로고
    • Defining the CREB regulon: A genome-wide analysis of transcription factor regulatory regions
    • S. Impey, S.R. McCorkle, H. Cha-Molstad, J.M. Dwyer, G.S. Yochum, and J.M. Boss Defining the CREB regulon: A genome-wide analysis of transcription factor regulatory regions Cell 119 7 2004 1041 1054
    • (2004) Cell , vol.119 , Issue.7 , pp. 1041-1054
    • Impey, S.1    McCorkle, S.R.2    Cha-Molstad, H.3    Dwyer, J.M.4    Yochum, G.S.5    Boss, J.M.6
  • 40
    • 55749094855 scopus 로고    scopus 로고
    • An integrated software system for analyzing ChIP-chip and ChIP-seq data
    • H. Ji, H. Jiang, W. Ma, D.S. Johnson, R.M. Myers, and W.H. Wong An integrated software system for analyzing ChIP-chip and ChIP-seq data Nature Biotechnology 26 11 2008 1293 1300
    • (2008) Nature Biotechnology , vol.26 , Issue.11 , pp. 1293-1300
    • Ji, H.1    Jiang, H.2    Ma, W.3    Johnson, D.S.4    Myers, R.M.5    Wong, W.H.6
  • 41
    • 34250159524 scopus 로고    scopus 로고
    • Genome-wide mapping of in vivo protein-DNA interactions
    • D.S. Johnson, A. Mortazavi, R.M. Myers, and B. Wold Genome-wide mapping of in vivo protein-DNA interactions Science (New York, NY) 316 5830 2007 1497 1502
    • (2007) Science (New York, NY) , vol.316 , Issue.5830 , pp. 1497-1502
    • Johnson, D.S.1    Mortazavi, A.2    Myers, R.M.3    Wold, B.4
  • 42
    • 52649132425 scopus 로고    scopus 로고
    • Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data
    • R. Jothi, S. Cuddapah, A. Barski, K. Cui, and K. Zhao Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data Nucleic Acids Research 36 16 2008 5221 5231
    • (2008) Nucleic Acids Research , vol.36 , Issue.16 , pp. 5221-5231
    • Jothi, R.1    Cuddapah, S.2    Barski, A.3    Cui, K.4    Zhao, K.5
  • 43
    • 79952273012 scopus 로고    scopus 로고
    • Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development
    • T. Kaplan, X.-Y. Li, P.J. Sabo, S. Thomas, J.A. Stamatoyannopoulos, and M.D. Biggin Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development PLoS Genetics 7 2 2011 e1001290
    • (2011) PLoS Genetics , vol.7 , Issue.2 , pp. 1001290
    • Kaplan, T.1    Li, X.-Y.2    Sabo, P.J.3    Thomas, S.4    Stamatoyannopoulos, J.A.5    Biggin, M.D.6
  • 44
    • 57449100870 scopus 로고    scopus 로고
    • Design and analysis of ChIP-seq experiments for DNA-binding proteins
    • P.V. Kharchenko, M.Y. Tolstorukov, and P.J. Park Design and analysis of ChIP-seq experiments for DNA-binding proteins Nature Biotechnology 26 12 2008 1351 1359
    • (2008) Nature Biotechnology , vol.26 , Issue.12 , pp. 1351-1359
    • Kharchenko, P.V.1    Tolstorukov, M.Y.2    Park, P.J.3
  • 45
    • 79955838994 scopus 로고    scopus 로고
    • A short survey of computational analysis methods in analysing ChIP-seq data
    • H. Kim, J. Kim, H. Selby, D. Gao, T. Tong, and T.L. Phang A short survey of computational analysis methods in analysing ChIP-seq data Human Genomics 5 2 2011 117 123
    • (2011) Human Genomics , vol.5 , Issue.2 , pp. 117-123
    • Kim, H.1    Kim, J.2    Selby, H.3    Gao, D.4    Tong, T.5    Phang, T.L.6
  • 46
    • 84872199826 scopus 로고    scopus 로고
    • MotifLab: A tools and data integration workbench for motif discovery and regulatory sequence analysis
    • K. Klepper, and F. Drabløs MotifLab: A tools and data integration workbench for motif discovery and regulatory sequence analysis BMC Bioinformatics 14 1 2013 9
    • (2013) BMC Bioinformatics , vol.14 , Issue.1 , pp. 9
    • Klepper, K.1    Drabløs, F.2
  • 48
    • 69849099700 scopus 로고    scopus 로고
    • Motif discovery and motif finding from genome-mapped DNase footprint data
    • I.V. Kulakovskiy, A.V. Favorov, and V.J. Makeev Motif discovery and motif finding from genome-mapped DNase footprint data Bioinformatics (Oxford, England) 25 18 2009 2318 2325
    • (2009) Bioinformatics (Oxford, England) , vol.25 , Issue.18 , pp. 2318-2325
    • Kulakovskiy, I.V.1    Favorov, A.V.2    Makeev, V.J.3
  • 50
    • 77952043585 scopus 로고    scopus 로고
    • Discovery of DNA motifs recognized by transcription factors through integration of different experimental sources
    • I.V. Kulakovskiy, and V.J. Makeev Discovery of DNA motifs recognized by transcription factors through integration of different experimental sources Biophysics 54 6 2010 667 674
    • (2010) Biophysics , vol.54 , Issue.6 , pp. 667-674
    • Kulakovskiy, I.V.1    Makeev, V.J.2
  • 53
    • 84874901934 scopus 로고    scopus 로고
    • Experimental and computational challenges from array-based to sequence-based ChIP techniques
    • X. Lan, and V. Jin Experimental and computational challenges from array-based to sequence-based ChIP techniques Current Bioinformatics 7 4 2012 7
    • (2012) Current Bioinformatics , vol.7 , Issue.4 , pp. 7
    • Lan, X.1    Jin, V.2
  • 55
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biology 10 3 2009 R25
    • (2009) Genome Biology , vol.10 , Issue.3 , pp. 25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 56
    • 79955023446 scopus 로고    scopus 로고
    • Processing and analyzing ChIP-seq data: From short reads to regulatory interactions
    • M. Leleu, G. Lefebvre, and J. Rougemont Processing and analyzing ChIP-seq data: From short reads to regulatory interactions Briefings in Functional Genomics 9 5-6 2010 466 476
    • (2010) Briefings in Functional Genomics , vol.9 , Issue.56 , pp. 466-476
    • Leleu, M.1    Lefebvre, G.2    Rougemont, J.3
  • 57
    • 40549106454 scopus 로고    scopus 로고
    • Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions
    • V.G. Levitsky, E.V. Ignatieva, E.A. Ananko, I.I. Turnaev, T.I. Merkulova, and N.A. Kolchanov Effective transcription factor binding site prediction using a combination of optimization, a genetic algorithm and discriminant analysis to capture distant interactions BMC Bioinformatics 8 2007 481
    • (2007) BMC Bioinformatics , vol.8 , pp. 481
    • Levitsky, V.G.1    Ignatieva, E.V.2    Ananko, E.A.3    Turnaev, I.I.4    Merkulova, T.I.5    Kolchanov, N.A.6
  • 58
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • H. Li, and R. Durbin Fast and accurate short read alignment with Burrows-Wheeler transform Bioinformatics 25 14 2009 1754 1760
    • (2009) Bioinformatics , vol.25 , Issue.14 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 59
    • 77957272611 scopus 로고    scopus 로고
    • A survey of sequence alignment algorithms for next-generation sequencing
    • H. Li, and N. Homer A survey of sequence alignment algorithms for next-generation sequencing Briefings in Bioinformatics 11 5 2010 473 483
    • (2010) Briefings in Bioinformatics , vol.11 , Issue.5 , pp. 473-483
    • Li, H.1    Homer, N.2
  • 60
    • 79953709415 scopus 로고    scopus 로고
    • The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding
    • X.-Y. Li, S. Thomas, P.J. Sabo, M.B. Eisen, J.A. Stamatoyannopoulos, and M.D. Biggin The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding Genome Biology 12 4 2011 R34
    • (2011) Genome Biology , vol.12 , Issue.4 , pp. 34
    • Li, X.-Y.1    Thomas, S.2    Sabo, P.J.3    Eisen, M.B.4    Stamatoyannopoulos, J.A.5    Biggin, M.D.6
  • 62
    • 46449123335 scopus 로고    scopus 로고
    • Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets
    • C. Linhart, Y. Halperin, and R. Shamir Transcription factor and microRNA motif discovery: The Amadeus platform and a compendium of metazoan target sets Genome Research 18 7 2008 1180 1189
    • (2008) Genome Research , vol.18 , Issue.7 , pp. 1180-1189
    • Linhart, C.1    Halperin, Y.2    Shamir, R.3
  • 63
    • 0035228215 scopus 로고    scopus 로고
    • BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
    • X. Liu, D.L. Brutlag, and J.S. Liu BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes Pacific symposium on biocomputing 2001 127 138
    • (2001) Pacific Symposium on Biocomputing , pp. 127-138
    • Liu, X.1    Brutlag, D.L.2    Liu, J.S.3
  • 64
    • 15544375816 scopus 로고    scopus 로고
    • DIP-chip: Rapid and accurate determination of DNA-binding specificity
    • X. Liu, D.M. Noll, J.D. Lieb, and N.D. Clarke DIP-chip: Rapid and accurate determination of DNA-binding specificity Genome Research 15 3 2005 421 427
    • (2005) Genome Research , vol.15 , Issue.3 , pp. 421-427
    • Liu, X.1    Noll, D.M.2    Lieb, J.D.3    Clarke, N.D.4
  • 65
    • 77953348282 scopus 로고    scopus 로고
    • Q&A: ChIP-seq technologies and the study of gene regulation
    • E.T. Liu, S. Pott, and M. Huss Q&A: ChIP-seq technologies and the study of gene regulation BMC Biology 8 1 2010 56
    • (2010) BMC Biology , vol.8 , Issue.1 , pp. 56
    • Liu, E.T.1    Pott, S.2    Huss, M.3
  • 67
    • 84860115916 scopus 로고    scopus 로고
    • A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information
    • X. Ma, A. Kulkarni, Z. Zhang, Z. Xuan, R. Serfling, and M.Q. Zhang A highly efficient and effective motif discovery method for ChIP-seq/ChIP-chip data using positional information Nucleic Acids Research 40 7 2012 e50
    • (2012) Nucleic Acids Research , vol.40 , Issue.7 , pp. 50
    • Ma, X.1    Kulkarni, A.2    Zhang, Z.3    Xuan, Z.4    Serfling, R.5    Zhang, M.Q.6
  • 69
    • 79951919856 scopus 로고    scopus 로고
    • An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq
    • E. Mercier, A. Droit, L. Li, G. Robertson, X. Zhang, and R. Gottardo An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq PLoS One 6 2 2011 e16432
    • (2011) PLoS One , vol.6 , Issue.2 , pp. 16432
    • Mercier, E.1    Droit, A.2    Li, L.3    Robertson, G.4    Zhang, X.5    Gottardo, R.6
  • 70
    • 38549135468 scopus 로고    scopus 로고
    • YEASTRACT-DISCOVERER: New tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae
    • DATABASE ISSUE
    • P.T. Monteiro, N.D. Mendes, M.C. Teixeira, S. d'Orey, S. Tenreiro, and N.P. Mira YEASTRACT-DISCOVERER: New tools to improve the analysis of transcriptional regulatory associations in Saccharomyces cerevisiae Nucleic Acids Research 36 Database issue 2008 D132 D136
    • (2008) Nucleic Acids Research , vol.36
    • Monteiro, P.T.1    Mendes, N.D.2    Teixeira, M.C.3    D'Orey, S.4    Tenreiro, S.5    Mira, N.P.6
  • 72
    • 2442704147 scopus 로고    scopus 로고
    • Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression
    • K. Murakami, T. Kojima, and Y. Sakaki Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression BMC Genomics 5 1 2004 16
    • (2004) BMC Genomics , vol.5 , Issue.1 , pp. 16
    • Murakami, K.1    Kojima, T.2    Sakaki, Y.3
  • 76
    • 33746207763 scopus 로고    scopus 로고
    • Multiplex sequencing of paired-end ditags (MS-PET): A strategy for the ultra-high-throughput analysis of transcriptomes and genomes
    • P. Ng, J.J.S. Tan, H.S. Ooi, Y.L. Lee, K.P. Chiu, and M.J. Fullwood Multiplex sequencing of paired-end ditags (MS-PET): A strategy for the ultra-high-throughput analysis of transcriptomes and genomes Nucleic Acids Research 34 12 2006 e84
    • (2006) Nucleic Acids Research , vol.34 , Issue.12 , pp. 84
    • Ng, P.1    Tan, J.J.S.2    Ooi, H.S.3    Lee, Y.L.4    Chiu, K.P.5    Fullwood, M.J.6
  • 77
    • 3242879525 scopus 로고    scopus 로고
    • SITECON: A tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition
    • WEB SERVER ISSUE
    • D.Y. Oshchepkov, E.E. Vityaev, D.A. Grigorovich, E.V. Ignatieva, and T.M. Khlebodarova SITECON: A tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition Nucleic Acids Research 32 Web Server issue 2004 W208 W212
    • (2004) Nucleic Acids Research , vol.32
    • Oshchepkov, D.Y.1    Vityaev, E.E.2    Grigorovich, D.A.3    Ignatieva, E.V.4    Khlebodarova, T.M.5
  • 78
    • 70349312354 scopus 로고    scopus 로고
    • ChIP-seq: Advantages and challenges of a maturing technology
    • P.J. Park ChIP-seq: Advantages and challenges of a maturing technology Nature Reviews. Genetics 10 10 2009 669 680
    • (2009) Nature Reviews. Genetics , vol.10 , Issue.10 , pp. 669-680
    • Park, P.J.1
  • 79
    • 70449711243 scopus 로고    scopus 로고
    • Computation for ChIP-seq and RNA-seq studies
    • S. Pepke, B. Wold, and A. Mortazavi Computation for ChIP-seq and RNA-seq studies Nature Methods 6 11 Suppl. 2009 S22 S32
    • (2009) Nature Methods , vol.6 , Issue.11 SUPPL.
    • Pepke, S.1    Wold, B.2    Mortazavi, A.3
  • 80
  • 81
    • 83255164884 scopus 로고    scopus 로고
    • Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution
    • H.S. Rhee, and B.F. Pugh Comprehensive genome-wide protein-DNA interactions detected at single-nucleotide resolution Cell 147 6 2011 1408 1419
    • (2011) Cell , vol.147 , Issue.6 , pp. 1408-1419
    • Rhee, H.S.1    Pugh, B.F.2
  • 83
    • 34547633677 scopus 로고    scopus 로고
    • Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing
    • G. Robertson, M. Hirst, M. Bainbridge, M. Bilenky, Y. Zhao, and T. Zeng Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing Nature Methods 4 8 2007 651 657
    • (2007) Nature Methods , vol.4 , Issue.8 , pp. 651-657
    • Robertson, G.1    Hirst, M.2    Bainbridge, M.3    Bilenky, M.4    Zhao, Y.5    Zeng, T.6
  • 85
    • 79952334870 scopus 로고    scopus 로고
    • A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs
    • M.B. Rye, P. Sætrom, and F. Drabløs A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs Nucleic Acids Research 39 4 2011 e25
    • (2011) Nucleic Acids Research , vol.39 , Issue.4 , pp. 25
    • Rye, M.B.1    Sætrom, P.2    Drabløs, F.3
  • 86
    • 77955869106 scopus 로고    scopus 로고
    • Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction
    • R.A. Salama, and D.J. Stekel Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction Nucleic Acids Research 38 12 2010 e135
    • (2010) Nucleic Acids Research , vol.38 , Issue.12 , pp. 135
    • Salama, R.A.1    Stekel, D.J.2
  • 87
    • 0347125328 scopus 로고    scopus 로고
    • JASPAR: An open-access database for eukaryotic transcription factor binding profiles
    • DATABASE ISSUE
    • A. Sandelin, W. Alkema, P. Engström, W.W. Wasserman, and B. Lenhard JASPAR: An open-access database for eukaryotic transcription factor binding profiles Nucleic Acids Research 32 Database issue 2004 D91 D94
    • (2004) Nucleic Acids Research , vol.32
    • Sandelin, A.1    Alkema, W.2    Engström, P.3    Wasserman, W.W.4    Lenhard, B.5
  • 88
    • 34247579156 scopus 로고    scopus 로고
    • A survey of motif discovery methods in an integrated framework
    • G.K. Sandve, and F. Drabløs A survey of motif discovery methods in an integrated framework Biology Direct 1 2006 11
    • (2006) Biology Direct , vol.1 , pp. 11
    • Sandve, G.K.1    Drabløs, F.2
  • 91
    • 13844275301 scopus 로고    scopus 로고
    • Similarity of position frequency matrices for transcription factor binding sites
    • D.E. Schones, P. Sumazin, and M.Q. Zhang Similarity of position frequency matrices for transcription factor binding sites Bioinformatics (Oxford, England) 21 3 2005 307 313
    • (2005) Bioinformatics (Oxford, England) , vol.21 , Issue.3 , pp. 307-313
    • Schones, D.E.1    Sumazin, P.2    Zhang, M.Q.3
  • 93
    • 84868674735 scopus 로고    scopus 로고
    • The limits of de novo DNA motif discovery
    • D. Simcha, N.D. Price, and D. Geman The limits of de novo DNA motif discovery PLoS One 7 11 2012 e47836
    • (2012) PLoS One , vol.7 , Issue.11 , pp. 47836
    • Simcha, D.1    Price, N.D.2    Geman, D.3
  • 94
    • 0037115891 scopus 로고    scopus 로고
    • Discovery of novel transcription factor binding sites by statistical overrepresentation
    • S. Sinha, and M. Tompa Discovery of novel transcription factor binding sites by statistical overrepresentation Nucleic Acids Research 30 24 2002 5549 5560
    • (2002) Nucleic Acids Research , vol.30 , Issue.24 , pp. 5549-5560
    • Sinha, S.1    Tompa, M.2
  • 95
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: Representation and discovery
    • G.D. Stormo DNA binding sites: Representation and discovery Bioinformatics (Oxford, England) 16 1 2000 16 23
    • (2000) Bioinformatics (Oxford, England) , vol.16 , Issue.1 , pp. 16-23
    • Stormo, G.D.1
  • 96
    • 84864425198 scopus 로고    scopus 로고
    • A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs
    • M. Thomas-Chollier, E. Darbo, C. Herrmann, M. Defrance, D. Thieffry, and J. Van Helden A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs Nature Protocols 7 8 2012 1551 1568
    • (2012) Nature Protocols , vol.7 , Issue.8 , pp. 1551-1568
    • Thomas-Chollier, M.1    Darbo, E.2    Herrmann, C.3    Defrance, M.4    Thieffry, D.5    Van Helden, J.6
  • 98
    • 21144439147 scopus 로고    scopus 로고
    • Assessing computational tools for the discovery of transcription factor binding sites
    • M. Tompa, N. Li, T.L. Bailey, G.M. Church, B. De Moor, and E. Eskin Assessing computational tools for the discovery of transcription factor binding sites Nature Biotechnology 23 1 2005 137 144
    • (2005) Nature Biotechnology , vol.23 , Issue.1 , pp. 137-144
    • Tompa, M.1    Li, N.2    Bailey, T.L.3    Church, G.M.4    De Moor, B.5    Eskin, E.6
  • 99
    • 39049165160 scopus 로고    scopus 로고
    • Efficient and accurate P-value computation for position weight matrices
    • H. Touzet, and J.-S. Varré Efficient and accurate P-value computation for position weight matrices Algorithms for Molecular Biology: AMB 2 2007 15
    • (2007) Algorithms for Molecular Biology: AMB , vol.2 , pp. 15
    • Touzet, H.1    Varré, J.-S.2
  • 100
    • 0025194307 scopus 로고
    • Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase
    • C. Tuerk, and L. Gold Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase Science (New York, NY) 249 4968 1990 505 510
    • (1990) Science (New York, NY) , vol.249 , Issue.4968 , pp. 505-510
    • Tuerk, C.1    Gold, L.2
  • 101
    • 73049112582 scopus 로고    scopus 로고
    • Extracting transcription factor targets from ChIP-Seq data
    • G. Tuteja, P. White, J. Schug, and K.H. Kaestner Extracting transcription factor targets from ChIP-Seq data Nucleic Acids Research 37 17 2009 e113
    • (2009) Nucleic Acids Research , vol.37 , Issue.17 , pp. 113
    • Tuteja, G.1    White, P.2    Schug, J.3    Kaestner, K.H.4
  • 102
  • 103
    • 0035093828 scopus 로고    scopus 로고
    • Chromatin profiling using targeted DNA adenine methyltransferase
    • B. Van Steensel, J. Delrow, and S. Henikoff Chromatin profiling using targeted DNA adenine methyltransferase Nature Genetics 27 3 2001 304 308
    • (2001) Nature Genetics , vol.27 , Issue.3 , pp. 304-308
    • Van Steensel, B.1    Delrow, J.2    Henikoff, S.3
  • 104
    • 23144460837 scopus 로고    scopus 로고
    • WordSpy: Identifying transcription factor binding motifs by building a dictionary and learning a grammar
    • WEB SERVER ISSUE
    • G. Wang, T. Yu, and W. Zhang WordSpy: Identifying transcription factor binding motifs by building a dictionary and learning a grammar Nucleic Acids Research 33 Web Server issue 2005 W412 W416
    • (2005) Nucleic Acids Research , vol.33
    • Wang, G.1    Yu, T.2    Zhang, W.3
  • 105
    • 84865852567 scopus 로고    scopus 로고
    • Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors
    • J. Wang, J. Zhuang, S. Iyer, X. Lin, T.W. Whitfield, and M.C. Greven Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors Genome Research 22 9 2012 1798 1812
    • (2012) Genome Research , vol.22 , Issue.9 , pp. 1798-1812
    • Wang, J.1    Zhuang, J.2    Iyer, S.3    Lin, X.4    Whitfield, T.W.5    Greven, M.C.6
  • 107
    • 1842584947 scopus 로고    scopus 로고
    • Applied bioinformatics for the identification of regulatory elements
    • W.W. Wasserman, and A. Sandelin Applied bioinformatics for the identification of regulatory elements Nature Reviews. Genetics 5 4 2004 276 287
    • (2004) Nature Reviews. Genetics , vol.5 , Issue.4 , pp. 276-287
    • Wasserman, W.W.1    Sandelin, A.2
  • 108
    • 84865508655 scopus 로고    scopus 로고
    • Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology
    • G. Wei, G. Hu, K. Cui, and K. Zhao Genome-wide mapping of nucleosome occupancy, histone modifications, and gene expression using next-generation sequencing technology Methods in Enzymology 513 2012 297 313
    • (2012) Methods in Enzymology , vol.513 , pp. 297-313
    • Wei, G.1    Hu, G.2    Cui, K.3    Zhao, K.4
  • 109
    • 30344478870 scopus 로고    scopus 로고
    • A global map of p53 transcription-factor binding sites in the human genome
    • C.-L. Wei, Q. Wu, V.B. Vega, K.P. Chiu, P. Ng, and T. Zhang A global map of p53 transcription-factor binding sites in the human genome Cell 124 1 2006 207 219
    • (2006) Cell , vol.124 , Issue.1 , pp. 207-219
    • Wei, C.-L.1    Wu, Q.2    Vega, V.B.3    Chiu, K.P.4    Ng, P.5    Zhang, T.6
  • 110
  • 112
    • 77955368935 scopus 로고    scopus 로고
    • Evaluation of algorithm performance in ChIP-seq peak detection
    • E.G. Wilbanks, and M.T. Facciotti Evaluation of algorithm performance in ChIP-seq peak detection PLoS One 5 7 2010 e11471
    • (2010) PLoS One , vol.5 , Issue.7 , pp. 11471
    • Wilbanks, E.G.1    Facciotti, M.T.2
  • 115
    • 58349110961 scopus 로고    scopus 로고
    • MotifMap: A human genome-wide map of candidate regulatory motif sites
    • X. Xie, P. Rigor, and P. Baldi MotifMap: A human genome-wide map of candidate regulatory motif sites Bioinformatics (Oxford, England) 25 2 2009 167 174
    • (2009) Bioinformatics (Oxford, England) , vol.25 , Issue.2 , pp. 167-174
    • Xie, X.1    Rigor, P.2    Baldi, P.3
  • 116
    • 84875590756 scopus 로고    scopus 로고
    • Motif discovery and transcription factor binding sites before and after the next-generation sequencing era
    • bbs016
    • F. Zambelli, G. Pesole, and G. Pavesi Motif discovery and transcription factor binding sites before and after the next-generation sequencing era Briefings in Bioinformatics 14 2 2013 225 237 bbs016
    • (2013) Briefings in Bioinformatics , vol.14 , Issue.2 , pp. 225-237
    • Zambelli, F.1    Pesole, G.2    Pavesi, G.3
  • 117
    • 84863866025 scopus 로고    scopus 로고
    • Improved models for transcription factor binding site identification using nonindependent interactions
    • Y. Zhao, S. Ruan, M. Pandey, and G.D. Stormo Improved models for transcription factor binding site identification using nonindependent interactions Genetics 191 3 2012 781 790
    • (2012) Genetics , vol.191 , Issue.3 , pp. 781-790
    • Zhao, Y.1    Ruan, S.2    Pandey, M.3    Stormo, G.D.4


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