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Volumn 1, Issue 1, 2005, Pages 0005-0013

Ab initio prediction of transcription factor targets using structural knowledge

Author keywords

[No Author keywords available]

Indexed keywords

BINDING SITES; TRANSCRIPTION;

EID: 29444434700     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0010001     Document Type: Article
Times cited : (97)

References (41)
  • 1
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: Representation and discovery
    • Stormo GD (2000) DNA binding sites: Representation and discovery. Bioinformatics 16: 16-23.
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 3
    • 0035393302 scopus 로고    scopus 로고
    • Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
    • Luscombe NM, Laskowski RA, Thornton JM (2001) Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res 29: 2860-2874.
    • (2001) Nucleic Acids Res , vol.29 , pp. 2860-2874
    • Luscombe, N.M.1    Laskowski, R.A.2    Thornton, J.M.3
  • 4
    • 0032524713 scopus 로고    scopus 로고
    • Quantitative parameters for amino acid-base interaction: Implications for prediction of protein-DNA binding sites
    • Mandel-Gutfreund Y, Margalit H (1998) Quantitative parameters for amino acid-base interaction: Implications for prediction of protein-DNA binding sites. Nucleic Acids Res 26: 2306-2312.
    • (1998) Nucleic Acids Res , vol.26 , pp. 2306-2312
    • Mandel-Gutfreund, Y.1    Margalit, H.2
  • 5
    • 0035221367 scopus 로고    scopus 로고
    • A structure-based approach for prediction of protein binding sites in gene upstream regions
    • Mandel-Gutfreund Y, Baron A, Margalit H (2001) A structure-based approach for prediction of protein binding sites in gene upstream regions. Pac Symp Biocomput 2001: 139-150.
    • (2001) Pac Symp Biocomput , vol.2001 , pp. 139-150
    • Mandel-Gutfreund, Y.1    Baron, A.2    Margalit, H.3
  • 6
    • 0027994717 scopus 로고
    • Toward a code for the interactions of zinc fingers with DNA: Selection of randomized fingers displayed on phage
    • Choo Y, Klug A (1994) Toward a code for the interactions of zinc fingers with DNA: Selection of randomized fingers displayed on phage. Proc Natl Acad Sei U S A 91: 11163-11167.
    • (1994) Proc Natl Acad Sei U S A , vol.91 , pp. 11163-11167
    • Choo, Y.1    Klug, A.2
  • 7
    • 0028046895 scopus 로고
    • Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions
    • Choo Y, Klug A (1994) Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. Proc Natl Acad Sei U S A 91: 11168-11172.
    • (1994) Proc Natl Acad Sei U S A , vol.91 , pp. 11168-11172
    • Choo, Y.1    Klug, A.2
  • 8
    • 0033120215 scopus 로고    scopus 로고
    • Structure-based prediction of DNA target sites by regulatory proteins
    • Kono H, Sarai A (1999) Structure-based prediction of DNA target sites by regulatory proteins. Proteins 35: 114-131.
    • (1999) Proteins , vol.35 , pp. 114-131
    • Kono, H.1    Sarai, A.2
  • 9
    • 0035865250 scopus 로고    scopus 로고
    • Expressing the human genome
    • Tupler R, Perini G, Green MR (2001) Expressing the human genome. Nature 409: 832-833.
    • (2001) Nature , vol.409 , pp. 832-833
    • Tupler, R.1    Perini, G.2    Green, M.R.3
  • 10
    • 0033524954 scopus 로고    scopus 로고
    • Analysis of zinc fingers optimized via phage display: Evaluating the utility of a recognition code
    • Wolfe SA, Greisman HA, Ramm EI, Pabo CO (1999) Analysis of zinc fingers optimized via phage display: Evaluating the utility of a recognition code. J Mol Biol 285: 1917-1934.
    • (1999) J Mol Biol , vol.285 , pp. 1917-1934
    • Wolfe, S.A.1    Greisman, H.A.2    Ramm, E.I.3    Pabo, C.O.4
  • 11
    • 0025773296 scopus 로고
    • Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1 A
    • Pavletich NP, Pabo CO (1991) Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1 A. Science 252: 809-817.
    • (1991) Science , vol.252 , pp. 809-817
    • Pavletich, N.P.1    Pabo, C.O.2
  • 12
    • 0032522662 scopus 로고    scopus 로고
    • High-resolution structures of variant Zif268-DNA complexes: Implications for understanding zinc finger-DNA recognition
    • Elrod-Erickson M, Benson TE, Pabo CO (1998) High-resolution structures of variant Zif268-DNA complexes: Implications for understanding zinc finger-DNA recognition. Structure 6: 451-464.
    • (1998) Structure , vol.6 , pp. 451-464
    • Elrod-Erickson, M.1    Benson, T.E.2    Pabo, C.O.3
  • 13
    • 0002629270 scopus 로고
    • Maximum likelihood from incomplete data via the em algorithm
    • Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm. J R Stat Soc Ser B 39: 1-38.
    • (1977) J R Stat Soc ser B , vol.39 , pp. 1-38
    • Dempster, A.P.1    Laird, N.M.2    Rubin, D.B.3
  • 14
    • 0035912721 scopus 로고    scopus 로고
    • Exploring the DNAbinding specificities of zinc fingers with DNA microarrays
    • Bulyk ML, Huang X, Choo Y, Church CM (2001) Exploring the DNAbinding specificities of zinc fingers with DNA microarrays. Proc Natl Acad Sei U S A 98: 7158-7163.
    • (2001) Proc Natl Acad Sei U S A , vol.98 , pp. 7158-7163
    • Bulyk, M.L.1    Huang, X.2    Choo, Y.3    Church, C.M.4
  • 15
    • 0036977044 scopus 로고    scopus 로고
    • Probabilistic code for DNA recognition by proteins of the EGR family
    • Benos PV, Lapedes AS, Stormo GD (2002) Probabilistic code for DNA recognition by proteins of the EGR family. J Mol Biol 323: 701-727.
    • (2002) J Mol Biol , vol.323 , pp. 701-727
    • Benos, P.V.1    Lapedes, A.S.2    Stormo, G.D.3
  • 16
    • 10744226888 scopus 로고    scopus 로고
    • Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs
    • Cawley S, Bekiranov S, Ng HH, Kapranov P, Sekinger EA, et al. (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116: 499-509.
    • (2004) Cell , vol.116 , pp. 499-509
    • Cawley, S.1    Bekiranov, S.2    Ng, H.H.3    Kapranov, P.4    Sekinger, E.A.5
  • 17
    • 0345148394 scopus 로고    scopus 로고
    • Common and diverged functions of the Drosophila gene pair D-Spl and buttonhead
    • Schock F, Purnell BA, Wimmer EA, Jackle H (1999) Common and diverged functions of the Drosophila gene pair D-Spl and buttonhead. Mech Dev 89: 125-132.
    • (1999) Mech Dev , vol.89 , pp. 125-132
    • Schock, F.1    Purnell, B.A.2    Wimmer, E.A.3    Jackle, H.4
  • 19
    • 0024316107 scopus 로고
    • The glass gene encodes a zinc-finger protein required by Drosopkila photoreceptor cells
    • Moses K, Ellis MC, Rubin GM (1989) The glass gene encodes a zinc-finger protein required by Drosopkila photoreceptor cells. Nature 340: 531-536.
    • (1989) Nature , vol.340 , pp. 531-536
    • Moses, K.1    Ellis, M.C.2    Rubin, G.M.3
  • 20
    • 0012252471 scopus 로고    scopus 로고
    • Systematic determination of patterns of gene expression during Drosophila embryogenesis
    • RESEARCH0088.
    • Tomancak P, Beaton A, Weiszmann R, Kwan E, Shu S, et al. (2002) Systematic determination of patterns of gene expression during Drosophila embryogenesis. Genome Biol 3: RESEARCH0088.
    • (2002) Genome Biol , vol.3
    • Tomancak, P.1    Beaton, A.2    Weiszmann, R.3    Kwan, E.4    Shu, S.5
  • 21
    • 0037183901 scopus 로고    scopus 로고
    • Gene expression during the life cycle of Drosophila melanogaster
    • Arbeitman MN, Furlong EE, Imam F, Johnson E, Null BH, et al. (2002) Gene expression during the life cycle of Drosophila melanogaster. Science 297: 2270-2275.
    • (2002) Science , vol.297 , pp. 2270-2275
    • Arbeitman, M.N.1    Furlong, E.E.2    Imam, F.3    Johnson, E.4    Null, B.H.5
  • 22
    • 0037249406 scopus 로고    scopus 로고
    • The FlyBase database of the Drosophila genome projects and community literature
    • FlyBase Consortium (2003) The FlyBase database of the Drosophila genome projects and community literature. Nucleic Acids Res 31: 172-175.
    • (2003) Nucleic Acids Res , vol.31 , pp. 172-175
  • 23
    • 0037327164 scopus 로고    scopus 로고
    • Discovery of genes with highly restricted expression patterns in the Drosophila wing disc using DNA oligonucleotide microarrays
    • Butler MJ, Jacobsen TL, Cain DM, Jarman MG, Hubank M, et al. (2003) Discovery of genes with highly restricted expression patterns in the Drosophila wing disc using DNA oligonucleotide microarrays. Development 130: 659-670.
    • (2003) Development , vol.130 , pp. 659-670
    • Butler, M.J.1    Jacobsen, T.L.2    Cain, D.M.3    Jarman, M.G.4    Hubank, M.5
  • 24
    • 0030795545 scopus 로고    scopus 로고
    • Epidermal muscle attachment site-specific target gene expression and interference with myotube guidance in response to ectopic stripe expression in the developing Drosophila epidermis
    • Vorbruggen G, Jackle H (1997) Epidermal muscle attachment site-specific target gene expression and interference with myotube guidance in response to ectopic stripe expression in the developing Drosophila epidermis. Proc Natl Acad Sei U S A 94: 8606-8611.
    • (1997) Proc Natl Acad Sei U S A , vol.94 , pp. 8606-8611
    • Vorbruggen, G.1    Jackle, H.2
  • 25
    • 0027937601 scopus 로고
    • Stereochemical basis of DNA recognition by Zn fingers
    • Suzuki M, Gerstein M, Yagi N (1994) Stereochemical basis of DNA recognition by Zn fingers. Nucleic Acids Res 22: 3397-3405.
    • (1994) Nucleic Acids Res , vol.22 , pp. 3397-3405
    • Suzuki, M.1    Gerstein, M.2    Yagi, N.3
  • 27
    • 4544293652 scopus 로고    scopus 로고
    • Toward an atomistic model for predicting transcription-factor binding sites
    • Endres RG, Schulthess TC, Wingree NS (2004) Toward an atomistic model for predicting transcription-factor binding sites. Proteins 57: 262-268.
    • (2004) Proteins , vol.57 , pp. 262-268
    • Endres, R.G.1    Schulthess, T.C.2    Wingree, N.S.3
  • 28
    • 7044239239 scopus 로고    scopus 로고
    • A simple physical model for the prediction and design of protein-DNA interactions
    • HavranekJJ, Duarte CM, Baker D (2004) A simple physical model for the prediction and design of protein-DNA interactions. J Mol Biol 344: 59-70.
    • (2004) J Mol Biol , vol.344 , pp. 59-70
    • Havranek, J.J.1    Duarte, C.M.2    Baker, D.3
  • 29
    • 13544274449 scopus 로고    scopus 로고
    • Looking into DNA recognition: Zinc finger binding specificity
    • Paillard G, Deremble C, Lavery R (2004) Looking into DNA recognition: Zinc finger binding specificity. Nucleic Acids Res 32: 6673-6682.
    • (2004) Nucleic Acids Res , vol.32 , pp. 6673-6682
    • Paillard, G.1    Deremble, C.2    Lavery, R.3
  • 30
    • 0032573426 scopus 로고    scopus 로고
    • A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome
    • Robison K, McGuire AM, Church GM (1998) A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J Mol Biol 284: 241-254.
    • (1998) J Mol Biol , vol.284 , pp. 241-254
    • Robison, K.1    McGuire, A.M.2    Church, G.M.3
  • 31
    • 0033081269 scopus 로고    scopus 로고
    • Using sequence logos and information analysis of Lrp DNA binding sites to investigate discrepancies between natural selection and SELEX
    • Shultzaberger RK, Schneider TD (1999) Using sequence logos and information analysis of Lrp DNA binding sites to investigate discrepancies between natural selection and SELEX. Nucleic Acids Res 27: 882-887.
    • (1999) Nucleic Acids Res , vol.27 , pp. 882-887
    • Shultzaberger, R.K.1    Schneider, T.D.2
  • 32
    • 0026497472 scopus 로고
    • Spl and the subfamily of zinc finger proteins with guaninerich binding sites
    • Berg JM (1992) Spl and the subfamily of zinc finger proteins with guaninerich binding sites. Proc Natl Acad Sei U S A 89: 11109-11110.
    • (1992) Proc Natl Acad Sei U S A , vol.89 , pp. 11109-11110
    • Berg, J.M.1
  • 33
    • 0037109192 scopus 로고    scopus 로고
    • Additivity in protein-DNA interactions: How good an approximation is it?
    • Benos PV, Bulyk ML, Stormo GD (2002) Additivity in protein-DNA interactions: How good an approximation is it? Nucleic Acids Res 30: 4442-4451.
    • (2002) Nucleic Acids Res , vol.30 , pp. 4442-4451
    • Benos, P.V.1    Bulyk, M.L.2    Stormo, G.D.3
  • 34
    • 0036493201 scopus 로고    scopus 로고
    • Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors
    • Bulyk ML, Johnson PLF, Church GM (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res 30: 1255-1261.
    • (2002) Nucleic Acids Res , vol.30 , pp. 1255-1261
    • Bulyk, M.L.1    Johnson, P.L.F.2    Church, G.M.3
  • 36
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14: 755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 38
    • 15844371193 scopus 로고    scopus 로고
    • CIS: Compound importance sampling method for protein-DNA binding site p-value estimation
    • Barash Y, Elidan G, Kaplan T, Friedman N (2005) CIS: compound importance sampling method for protein-DNA binding site p-value estimation. Bioinformatics. 21: 596-600.
    • (2005) Bioinformatics. , vol.21 , pp. 596-600
    • Barash, Y.1    Elidan, G.2    Kaplan, T.3    Friedman, N.4
  • 39
    • 0001677717 scopus 로고
    • Controlling the false discovery rate: A practical and powerful approach to multiple testing
    • Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J R Stat Soc Ser B 57: 289-300.
    • (1995) J R Stat Soc ser B , vol.57 , pp. 289-300
    • Benjamini, Y.1    Hochberg, Y.2
  • 41
    • 0026754698 scopus 로고
    • Sequence-specific recognition of DNA by zinc-finger peptides derived from the transcription factor Spl
    • Kriwacki RW, Schultz SC, Steitz TA, CaradonnaJP (1992) Sequence-specific recognition of DNA by zinc-finger peptides derived from the transcription factor Spl. Proc Natl Acad Sei U S A 89: 9759-9763.
    • (1992) Proc Natl Acad Sei U S A , vol.89 , pp. 9759-9763
    • Kriwacki, R.W.1    Schultz, S.C.2    Steitz, T.A.3    Caradonna, J.P.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.