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Volumn 2007, Issue , 2007, Pages

Motif discovery in tissue-specific regulatory sequences using directed information

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EID: 38749112559     PISSN: 16874145     EISSN: 16874153     Source Type: Journal    
DOI: 10.1155/2007/13853     Document Type: Article
Times cited : (26)

References (42)
  • 1
    • 33646229522 scopus 로고    scopus 로고
    • Practical strategies for discovering regulatory DNA sequence motifs
    • fraenkel-admin@mit.edu
    • K. D. MacIsaac E. Fraenkel fraenkel-admin@mit.edu Practical strategies for discovering regulatory DNA sequence motifs. PLoS Computational Biology 2 4 2006 e36
    • (2006) PLoS Computational Biology , vol.2 , Issue.4
    • MacIsaac, K.D.1    Fraenkel, E.2
  • 2
    • 3042731990 scopus 로고    scopus 로고
    • Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes
    • kreiman@mit.edu
    • G. Kreiman kreiman@mit.edu Identification of sparsely distributed clusters of cis-regulatory elements in sets of co-expressed genes. Nucleic Acids Research 32 9 2004 2889 2900
    • (2004) Nucleic Acids Research , vol.32 , Issue.9 , pp. 2889-2900
    • Kreiman, G.1
  • 3
    • 0031586003 scopus 로고    scopus 로고
    • Prediction of complete gene structures in human genomic DNA
    • C. Burge S. Karlin Prediction of complete gene structures in human genomic DNA. Journal of Molecular Biology 268 1 1997 78 94
    • (1997) Journal of Molecular Biology , vol.268 , Issue.1 , pp. 78-94
    • Burge, C.1    Karlin, S.2
  • 4
    • 33645887244 scopus 로고    scopus 로고
    • Chromatin looping and the probability of transcription
    • li111640@u.washington.edu
    • Q. Li li111640@u.washington.edu G. Barkess H. Qian Chromatin looping and the probability of transcription. Trends in Genetics 22 4 2006 197 202
    • (2006) Trends in Genetics , vol.22 , Issue.4 , pp. 197-202
    • Li, Q.1    Barkess, G.2    Qian, H.3
  • 5
    • 11144339384 scopus 로고    scopus 로고
    • Long-range control of gene expression: Emerging mechanisms and disruption in disease
    • v.vanheyningen@hgu.mrc.ac.uk
    • D. A. Kleinjan V. van Heyningen v.vanheyningen@hgu.mrc.ac.uk Long-range control of gene expression: emerging mechanisms and disruption in disease. The American Journal of Human Genetics 76 1 2005 8 32
    • (2005) The American Journal of Human Genetics , vol.76 , Issue.1 , pp. 8-32
    • Kleinjan, D.A.1    Van Heyningen, V.2
  • 6
    • 33846876333 scopus 로고    scopus 로고
    • Predicting tissue-specific enhancers in the human genome
    • ovcharenko1@llnl.gov
    • L. A. Pennacchio G. G. Loots M. A. Nobrega I. Ovcharenko ovcharenko1@llnl.gov Predicting tissue-specific enhancers in the human genome. Genome Research 17 2 2007 201 211
    • (2007) Genome Research , vol.17 , Issue.2 , pp. 201-211
    • Pennacchio, L.A.1    Loots, G.G.2    Nobrega, M.A.3    Ovcharenko, I.4
  • 7
    • 23744493161 scopus 로고    scopus 로고
    • Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences
    • rch8@psu.edu
    • D. C. King J. Taylor L. Elnitski F. Chiaromonte W. Miller R. C. Hardison rch8@psu.edu Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences. Genome Research 15 8 2005 1051 1060
    • (2005) Genome Research , vol.15 , Issue.8 , pp. 1051-1060
    • King, D.C.1    Taylor, J.2    Elnitski, L.3    Chiaromonte, F.4    Miller, W.5    Hardison, R.C.6
  • 8
    • 33751316959 scopus 로고    scopus 로고
    • In vivo enhancer analysis of human conserved non-coding sequences
    • LAPennacchio@lbl.gov
    • L. A. Pennacchio LAPennacchio@lbl.gov N. Ahituv A. M. Moses In vivo enhancer analysis of human conserved non-coding sequences. Nature 444 7118 2006 499 502
    • (2006) Nature , vol.444 , Issue.7118 , pp. 499-502
    • Pennacchio, L.A.1    Ahituv, N.2    Moses, A.M.3
  • 9
    • 33745951206 scopus 로고    scopus 로고
    • ROKU: A novel method for indentification of tissue-specific genes
    • tterada@iu.a.u-tokyo.ac.jp yunakai@iu.a.u-tokyo.ac.jp ye@bi.a.u-tokyo.ac.jp kadota@iu.a.u-tokyo.ac.jp shimizu@bi.a.u-tokyo.ac.jp
    • K. Kadota kadota@iu.a.u-tokyo.ac.jp J. Ye ye@bi.a.u-tokyo.ac.jp Y. Nakai yunakai@iu.a.u-tokyo.ac.jp T. Terada tterada@iu.a.u-tokyo.ac.jp K. Shimizu shimizu@bi.a.u-tokyo.ac.jp ROKU: a novel method for indentification of tissue-specific genes. BMC Bioinformatics 7 2006 294
    • (2006) BMC Bioinformatics , vol.7 , pp. 294
    • Kadota, K.1    Ye, J.2    Nakai, Y.3    Terada, T.4    Shimizu, K.5
  • 11
    • 33846057516 scopus 로고    scopus 로고
    • Regulatory networks: Linking microarray data to systems biology
    • Werner@genomatix.de
    • T. Werner Werner@genomatix.de Regulatory networks: linking microarray data to systems biology. Mechanisms of Ageing and Development 128 1 2007 168 172
    • (2007) Mechanisms of Ageing and Development , vol.128 , Issue.1 , pp. 168-172
    • Werner, T.1
  • 12
    • 23144431920 scopus 로고    scopus 로고
    • TOUCAN 2: The all-inclusive open source workbench for regulatory sequence analysis
    • stein.aerts@med.kuleuven.ac.be
    • S. Aerts stein.aerts@med.kuleuven.ac.be P. Van Loo G. Thijs TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. Nucleic Acids Research 33, (Web Server Issue) 2005 W393 W396
    • (2005) Nucleic Acids Research , vol.33
    • Aerts, S.1    Van Loo, P.2    Thijs, G.3
  • 13
    • 27744473016 scopus 로고    scopus 로고
    • Using hexamers to predict cis-regulatory motifs in Drosophila
    • bobc@ics.uci.edu kibler@ics.uci.edu
    • B. Y. Chan bobc@ics.uci.edu D. Kibler kibler@ics.uci.edu Using hexamers to predict cis-regulatory motifs in Drosophila. BMC Bioinformatics 6 2005 262
    • (2005) BMC Bioinformatics , vol.6 , pp. 262
    • Chan, B.Y.1    Kibler, D.2
  • 14
    • 0030461607 scopus 로고    scopus 로고
    • The prediction of vertebrate promoter regions using differential hexamer frequency analysis
    • hutch@netshop.bc.ca
    • G. B. Hutchinson hutch@netshop.bc.ca The prediction of vertebrate promoter regions using differential hexamer frequency analysis. Computer Applications in the Biosciences 12 5 1996 391 398
    • (1996) Computer Applications in the Biosciences , vol.12 , Issue.5 , pp. 391-398
    • Hutchinson, G.B.1
  • 16
    • 0032938120 scopus 로고    scopus 로고
    • Localization of distant urogenital system-, central nervous system-, and endocardium-specific transcriptional regulatory elements in the GATA-3 locus
    • G. Lakshmanan K. H. Lieuw K.-C. Lim Localization of distant urogenital system-, central nervous system-, and endocardium-specific transcriptional regulatory elements in the GATA-3 locus. Molecular and Cellular Biology 19 2 1999 1558 1568
    • (1999) Molecular and Cellular Biology , vol.19 , Issue.2 , pp. 1558-1568
    • Lakshmanan, G.1    Lieuw, K.H.2    Lim, K.-C.3
  • 17
    • 8644243022 scopus 로고    scopus 로고
    • Multiple, distant Gata2 enhancers specify temporally and tissue-specific patterning in the developing urogenital system
    • engel@umich.edu
    • M. Khandekar N. Suzuki J. Lewton M. Yamamoto J. D. Engel engel@umich.edu Multiple, distant Gata2 enhancers specify temporally and tissue-specific patterning in the developing urogenital system. Molecular and Cellular Biology 24 23 2004 10263 10276
    • (2004) Molecular and Cellular Biology , vol.24 , Issue.23 , pp. 10263-10276
    • Khandekar, M.1    Suzuki, N.2    Lewton, J.3    Yamamoto, M.4    Engel, J.D.5
  • 18
    • 24344458137 scopus 로고    scopus 로고
    • Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy
    • flong@lbl.gov hpeng@lbl.gov CHQDing@lbl.gov
    • H. Peng hpeng@lbl.gov F. Long flong@lbl.gov C. Ding CHQDing@lbl.gov Feature selection based on mutual information criteria of max-dependency, max-relevance, and min-redundancy. IEEE Transactions on Pattern Analysis and Machine Intelligence 27 8 2005 1226 1238
    • (2005) IEEE Transactions on Pattern Analysis and Machine Intelligence , vol.27 , Issue.8 , pp. 1226-1238
    • Peng, H.1    Long, F.2    Ding, C.3
  • 21
    • 0015737911 scopus 로고
    • The bidirectional communication theory - A generalization of information theory
    • H. Marko The bidirectional communication theory - a generalization of information theory. IEEE Transactions on Communications COM-21 12 1973 1345 1351
    • (1973) IEEE Transactions on Communications , vol.21 , Issue.12 , pp. 1345-1351
    • Marko, H.1
  • 23
    • 34249819354 scopus 로고    scopus 로고
    • Source coding with feed-forward: Rate-distortion theorems and error exponents for a general source
    • rvenkata@eecs.umich.edu pradhanv@eecs.umich.edu
    • R. Venkataramanan rvenkata@eecs.umich.edu S. S. Pradhan pradhanv@eecs.umich.edu Source coding with feed-forward: rate-distortion theorems and error exponents for a general source. IEEE Transactions on Information Theory 53 6 2007 2154 2179
    • (2007) IEEE Transactions on Information Theory , vol.53 , Issue.6 , pp. 2154-2179
    • Venkataramanan, R.1    Pradhan, S.S.2
  • 28
    • 0041877169 scopus 로고    scopus 로고
    • Estimation of entropy and mutual information
    • liam@cns.nyu.edu
    • L. Paninski liam@cns.nyu.edu Estimation of entropy and mutual information. Neural Computation 15 6 2003 1191 1253
    • (2003) Neural Computation , vol.15 , Issue.6 , pp. 1191-1253
    • Paninski, L.1
  • 29
    • 68349153730 scopus 로고
    • Relative entropy measures of multivariate dependence
    • H. Joe Relative entropy measures of multivariate dependence. Journal of the American Statistical Association 84 1989 405 157 164
    • (1989) Journal of the American Statistical Association , vol.84 , Issue.405 , pp. 157-164
    • Joe, H.1
  • 30
    • 0003991665 scopus 로고
    • Monographs on Statistics and Applied ProbabilityChapman & Hall/CRC Boca Raton, Fla, USA
    • B. Efron R. J. Tibshirani An Introduction to the Bootstrap. Monographs on Statistics and Applied Probability Chapman & Hall/CRC Boca Raton, Fla, USA 1994
    • (1994) An Introduction to the Bootstrap
    • Efron, B.1    Tibshirani, R.J.2
  • 32
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Y. Benjamini Y. Hochberg Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society. Series B 57 1995 1 289 300
    • (1995) Journal of the Royal Statistical Society. Series B , vol.57 , Issue.1 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 34
    • 0002282074 scopus 로고
    • A new measure of rank correlation
    • M. G. Kendall A new measure of rank correlation. Biometrika 30 1938 1/2 81 93
    • (1938) Biometrika , vol.30 , Issue.12 , pp. 81-93
    • Kendall, M.G.1
  • 35
    • 38749128854 scopus 로고    scopus 로고
    • NCBI Pubmed URL http://www.ncbi.nlm.nih.gov/entrez/query.fcgi
    • Pubmed Url, N.1
  • 36
    • 0031052775 scopus 로고    scopus 로고
    • Regulation of the rat cardiac troponin i gene by the transcription factor GATA-4
    • A. M. Murphy W. R. Thompson L. F. Peng L. Jones II Regulation of the rat cardiac troponin I gene by the transcription factor GATA-4. Biochemical Journal 322, part 2 1997 393 401
    • (1997) Biochemical Journal , vol.3222 , pp. 393-401
    • Murphy, A.M.1    Thompson, W.R.2    Peng, L.F.3    Jones, I.I.L.4
  • 37
    • 33751396373 scopus 로고    scopus 로고
    • Myocardial transcription factors are modulated during pathologic cardiac hypertrophy in vivo
    • azakiet@surgery.ucsf.edu
    • A. Azakie azakiet@surgery.ucsf.edu J. R. Fineman Y. He Myocardial transcription factors are modulated during pathologic cardiac hypertrophy in vivo. The Journal of Thoracic and Cardiovascular Surgery 132 6 2006 1262 1271.e4
    • (2006) The Journal of Thoracic and Cardiovascular Surgery , vol.132 , Issue.6
    • Azakie, A.1    Fineman, J.R.2    He, Y.3
  • 38
    • 0035895948 scopus 로고    scopus 로고
    • Opposing roles of Elk-1 and its brain-specific usoform, short Elk-1, in nerve growth factor-induced PC12 differentiation
    • P. Vanhoutte J. L. Nissen B. Brugg Opposing roles of Elk-1 and its brain-specific usoform, short Elk-1, in nerve growth factor-induced PC12 differentiation. Journal of Biological Chemistry 276 7 2001 5189 5196
    • (2001) Journal of Biological Chemistry , vol.276 , Issue.7 , pp. 5189-5196
    • Vanhoutte, P.1    Nissen, J.L.2    Brugg, B.3
  • 39
    • 0027327918 scopus 로고
    • Regulation of muscle transcription by the MyoD family: The heart of the matter
    • E. N. Olson Regulation of muscle transcription by the MyoD family: the heart of the matter. Circulation Research 72 1 1993 1 6
    • (1993) Circulation Research , vol.72 , Issue.1 , pp. 1-6
    • Olson, E.N.1
  • 41
    • 31644438184 scopus 로고    scopus 로고
    • Pax2/8-regulated Gata3 expression is necessary for morphogenesis and guidance of the nephric duct in the developing kidney
    • maxime.bouchard@mcgill.ca
    • D. Grote A. Souabni M. Busslinger M. Bouchard maxime.bouchard@mcgill.ca Pax2/8-regulated Gata3 expression is necessary for morphogenesis and guidance of the nephric duct in the developing kidney. Development 133 1 2006 53 61
    • (2006) Development , vol.133 , Issue.1 , pp. 53-61
    • Grote, D.1    Souabni, A.2    Busslinger, M.3    Bouchard, M.4


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