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Volumn 7, Issue 1, 2006, Pages 48-54

Studying statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in the eukaryotic genomes

Author keywords

Regulatory regions; Statistical methods; Transcription factor binding sites

Indexed keywords

DNA; TRANSCRIPTION FACTOR;

EID: 33748786226     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbk004     Document Type: Review
Times cited : (5)

References (90)
  • 1
    • 0033775978 scopus 로고    scopus 로고
    • Human-mouse genome comparisons to locate regulatory sites
    • Wasserman W, Palumbo M, Thompson W, et al. Human-mouse genome comparisons to locate regulatory sites. Nat Genet 2000;26:225-28.
    • (2000) Nat Genet , vol.26 , pp. 225-228
    • Wasserman, W.1    Palumbo, M.2    Thompson, W.3
  • 2
    • 0035986888 scopus 로고    scopus 로고
    • Evolution of transcription factor binding sites in mammalian gene regulatory regions: Conservation and turnover
    • Dermitzakis ET, Clark AG. Evolution of transcription factor binding sites in mammalian gene regulatory regions: Conservation and turnover. Mol Biol Evol 2002;19:1114-21.
    • (2002) Mol Biol Evol , vol.19 , pp. 1114-1121
    • Dermitzakis, E.T.1    Clark, A.G.2
  • 3
    • 0032549745 scopus 로고    scopus 로고
    • Genomic cis-regulatory logic: Functional analysis and computational model of a sea urchin gene control system
    • Yuh C, Bolouri H, Davidson E. Genomic cis-regulatory logic: Functional analysis and computational model of a sea urchin gene control system. Science 1998;279:1896-1902.
    • (1998) Science , vol.279 , pp. 1896-1902
    • Yuh, C.1    Bolouri, H.2    Davidson, E.3
  • 5
    • 0036500609 scopus 로고    scopus 로고
    • A genomic regulatory network for development
    • Davidson E, Rast JP, Oliveri P, et al. A genomic regulatory network for development. Science 2002;295:1669-78.
    • (2002) Science , vol.295 , pp. 1669-1678
    • Davidson, E.1    Rast, J.P.2    Oliveri, P.3
  • 6
    • 0021113913 scopus 로고
    • On the determination of deoxyribonucleic acid-protein interaction parameters using the nitrocellulose filter-binding assay
    • Woodbury CJ, von Hippel P. On the determination of deoxyribonucleic acid-protein interaction parameters using the nitrocellulose filter-binding assay. Biochemistry 1983;22: 4730-37.
    • (1983) Biochemistry , vol.22 , pp. 4730-4737
    • Woodbury, C.J.1    von Hippel, P.2
  • 7
    • 0019877067 scopus 로고
    • A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: Application to components of the Escherichia coli lactose operon regulatory system
    • Garner M, Revzin A. A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: Application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res 1981;9:3047-60.
    • (1981) Nucleic Acids Res , vol.9 , pp. 3047-3060
    • Garner, M.1    Revzin, A.2
  • 8
    • 0027327521 scopus 로고
    • A role in DNA binding for the linker sequences of the first three zinc fingers of TFIIIA
    • Choo Y, Klug A. A role in DNA binding for the linker sequences of the first three zinc fingers of TFIIIA. Nucleic Acids Res 1993;21:3341-46.
    • (1993) Nucleic Acids Res , vol.21 , pp. 3341-3346
    • Choo, Y.1    Klug, A.2
  • 9
    • 0018199224 scopus 로고
    • DNAse footprinting: A simple method for the detection of protein-DNA binding specificity
    • Galas D, Schmitz A. DNAse footprinting: A simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res 1978;5:3157-70.
    • (1978) Nucleic Acids Res , vol.5 , pp. 3157-3170
    • Galas, D.1    Schmitz, A.2
  • 10
    • 0029093857 scopus 로고
    • Quantification of DNA-protein interaction by UV cross-linking
    • Molnar G, OLeary N, Pardee A, et al. Quantification of DNA-protein interaction by UV cross-linking. Nucleic Acids Res 1995;23:3318-26.
    • (1995) Nucleic Acids Res , vol.23 , pp. 3318-3326
    • Molnar, G.1    OLeary, N.2    Pardee, A.3
  • 11
    • 0026023608 scopus 로고
    • A genetic model for interaction of the homeodomain recognition helix with DNA
    • Hanes S, Brent R. A genetic model for interaction of the homeodomain recognition helix with DNA. Science 1991; 251:426-30.
    • (1991) Science , vol.251 , pp. 426-430
    • Hanes, S.1    Brent, R.2
  • 12
    • 0034704248 scopus 로고    scopus 로고
    • Genome-wide location and function of DNA binding proteins
    • Ren B, Robert F, Wyrick J, et al. Genome-wide location and function of DNA binding proteins. Science 2000;290: 2306-9.
    • (2000) Science , vol.290 , pp. 2306-2309
    • Ren, B.1    Robert, F.2    Wyrick, J.3
  • 13
    • 0028046895 scopus 로고
    • Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions
    • Choo Y, Klug A. Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. Proc Natl Acad Sci USA 1994;91: 11168-72.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 11168-11172
    • Choo, Y.1    Klug, A.2
  • 14
    • 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. Toward a code for the interactions of zinc fingers with DNA: Selection of randomized fingers displayed on phage. Proc Natl Acad Sci USA 1994; 91:11163-67.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 11163-11167
    • Choo, Y.1    Klug, A.2
  • 15
    • 0033028741 scopus 로고    scopus 로고
    • Quantifying DNA-protein interactions by double-stranded DNA arrays
    • Bulyk M, Gentalen E, Lockhart D, et al. Quantifying DNA-protein interactions by double-stranded DNA arrays. Nat Biotechnol 1999;17:573-77.
    • (1999) Nat Biotechnol , vol.17 , pp. 573-577
    • Bulyk, M.1    Gentalen, E.2    Lockhart, D.3
  • 16
    • 0027974851 scopus 로고
    • 1.9 A resolution refined structure of TBP recognizing the minor groove of TATAAAAG
    • Kim J, Burley S. 1.9 A resolution refined structure of TBP recognizing the minor groove of TATAAAAG. Nat Struct Biol 1994;1:638-53.
    • (1994) Nat Struct Biol , vol.1 , pp. 638-653
    • Kim, J.1    Burley, S.2
  • 17
    • 0042697343 scopus 로고    scopus 로고
    • The Evolution of transcriptional regulation in eukaryotes
    • Wray L, Hahn M, Abouheif E, et al. The Evolution of transcriptional regulation in eukaryotes. Molec Bio Evol 2003; 20:1377-1419.
    • (2003) Molec Bio Evol , vol.20 , pp. 1377-1419
    • Wray, L.1    Hahn, M.2    Abouheif, E.3
  • 18
    • 0030986188 scopus 로고    scopus 로고
    • The hardwiring of development: Organization and function of genomic regulatory system
    • Arnone M, Davidson EH. The hardwiring of development: Organization and function of genomic regulatory system. Development 1997;124:1851-64.
    • (1997) Development , vol.124 , pp. 1851-1864
    • Arnone, M.1    Davidson, E.H.2
  • 19
    • 0032413411 scopus 로고    scopus 로고
    • Pedicting gene regulatory elements in silico on a genomic scale
    • Brazma A, Jonassen I, Vilo J, et al. Pedicting gene regulatory elements in silico on a genomic scale. Genome Res 1998;8: 1202-15.
    • (1998) Genome Res , vol.8 , pp. 1202-1215
    • Brazma, A.1    Jonassen, I.2    Vilo, J.3
  • 20
    • 0037154218 scopus 로고    scopus 로고
    • Genome wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo
    • Markstein M, Markstein P, Markstein V, et al. Genome wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo. PNAS 2002; 99:763-68.
    • (2002) PNAS , vol.99 , pp. 763-768
    • Markstein, M.1    Markstein, P.2    Markstein, V.3
  • 21
    • 0041389077 scopus 로고    scopus 로고
    • Identification of functional lists of transcription factor binding motifs in genome sequences: The MSCAN algorithm
    • Johansson O, Alkema W, Wasserman WW, et al. Identification of functional lists of transcription factor binding motifs in genome sequences: The MSCAN algorithm. Bioinformatics 2003;19(Suppl.):I169-76.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL.
    • Johansson, O.1    Alkema, W.2    Wasserman, W.W.3
  • 22
    • 2942576308 scopus 로고    scopus 로고
    • Computational detection of genomic cis-regulatory modules, applied to body patterning in the early Drosophila embryo
    • Rajewski N, Vergassola W, Gaul U, et al. Computational detection of genomic cis-regulatory modules, applied to body patterning in the early Drosophila embryo. BMC Bioinformatics 2002;3:30.
    • (2002) BMC Bioinformatics , vol.3 , pp. 30
    • Rajewski, N.1    Vergassola, W.2    Gaul, U.3
  • 23
    • 0002759539 scopus 로고    scopus 로고
    • Unsupervised learning of multiple motifs in biopolymers using expectation maximization
    • (MEME)
    • Bailey T, Elkan C. Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning 2003;21:51-80 (MEME).
    • (2003) Machine Learning , vol.21 , pp. 51-80
    • Bailey, T.1    Elkan, C.2
  • 24
    • 0037398319 scopus 로고    scopus 로고
    • Homotypic regulatory lists in Drosophila
    • Lifanov AP, Makeev VJ, Nazina AG, et al. Homotypic regulatory lists in Drosophila. Genome Res 2003;13: 579-88.
    • (2003) Genome Res , vol.13 , pp. 579-588
    • Lifanov, A.P.1    Makeev, V.J.2    Nazina, A.G.3
  • 25
    • 0037154273 scopus 로고    scopus 로고
    • Exploiting TFBS clustering to identify CRM involved in pattern formation in Drosophila genome
    • Berman B, Nibu Y, Pfeiffer P, et al. Exploiting TFBS clustering to identify CRM involved in pattern formation in Drosophila genome. PNAS 2002;99:757-62.
    • (2002) PNAS , vol.99 , pp. 757-762
    • Berman, B.1    Nibu, Y.2    Pfeiffer, P.3
  • 26
    • 0034363522 scopus 로고    scopus 로고
    • The TRANSFAC System on Gene Regulation
    • Wingender E. The TRANSFAC System on Gene Regulation. Trends in Glycoscience and Glycotechnology 2000;12:255-264. http://www.gene-regulation.com/pub/databases.html.
    • (2000) Trends in Glycoscience and Glycotechnology , vol.12 , pp. 255-264
    • Wingender, E.1
  • 27
    • 1642289044 scopus 로고    scopus 로고
    • Coordinate enhancers share common organization features in the Drosophila genome
    • Erives A, Levine M. Coordinate enhancers share common organization features in the Drosophila genome. Proc Natl Acad Sci USA 2004;101:3851-56.
    • (2004) Proc Natl Acad Sci USA , vol.101 , pp. 3851-3856
    • Erives, A.1    Levine, M.2
  • 28
    • 0344442419 scopus 로고    scopus 로고
    • Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information
    • Makeev VJ, Lifanov AP, Nazina AG, et al. Distance preferences in the arrangement of binding motifs and hierarchical levels in organization of transcription regulatory information. Nucleic Acids Res 2003;31:6016-26.
    • (2003) Nucleic Acids Res , vol.31 , pp. 6016-6026
    • Makeev, V.J.1    Lifanov, A.P.2    Nazina, A.G.3
  • 29
    • 0033954325 scopus 로고    scopus 로고
    • COMPEL: A database on composite regulatory elements providing combinatorial transcriptional regulation
    • Kel-Margoulis OV, Romanshchenko AG, Kolchanov NA, et al. COMPEL: A database on composite regulatory elements providing combinatorial transcriptional regulation. Nucleic Acids Res 2000;28:311-15.
    • (2000) Nucleic Acids Res , vol.28 , pp. 311-315
    • Kel-Margoulis, O.V.1    Romanshchenko, A.G.2    Kolchanov, N.A.3
  • 30
    • 0030927867 scopus 로고    scopus 로고
    • Searching for regulatory elements in human non coding sequences
    • Duret L, Bucher P. Searching for regulatory elements in human non coding sequences. Curr Opin Struct Biol 1997;7:399-406.
    • (1997) Curr Opin Struct Biol , vol.7 , pp. 399-406
    • Duret, L.1    Bucher, P.2
  • 32
    • 0037263797 scopus 로고    scopus 로고
    • Strategies and tools for whole-genome alignments
    • Couronne O, Poliakov A, Bray N, et al. Strategies and tools for whole-genome alignments. Genome Res 2003;13:73-80.
    • (2003) Genome Res , vol.13 , pp. 73-80
    • Couronne, O.1    Poliakov, A.2    Bray, N.3
  • 33
    • 0242418246 scopus 로고    scopus 로고
    • Phylogenetic shadowing of primate sequences to find functional regions of the human genome
    • Boffelli D, McAuliffe J, Ovcharenko D, et al. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 2002;299:1391-4.
    • (2002) Science , vol.299 , pp. 1391-1394
    • Boffelli, D.1    McAuliffe, J.2    Ovcharenko, D.3
  • 34
    • 18344415808 scopus 로고    scopus 로고
    • Distinguishing regulatory DNA from neutral sites
    • Elnitski L, Hardison RC, Li J, et al. Distinguishing regulatory DNA from neutral sites. Genome Res 2003;13:64-72.
    • (2003) Genome Res , vol.13 , pp. 64-72
    • Elnitski, L.1    Hardison, R.C.2    Li, J.3
  • 35
    • 12744263842 scopus 로고    scopus 로고
    • Computational identification of developmental enhancers: Conservation and function of TFBS clusters in Drosophila melanogaster and Drosophila pseudoobscura
    • Berman BP, Pfeiffer B, Laverty RT, et al. Computational identification of developmental enhancers: Conservation and function of TFBS clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biology 2004;5:R61.
    • (2004) Genome Biology , vol.5
    • Berman, B.P.1    Pfeiffer, B.2    Laverty, R.T.3
  • 36
    • 20044366725 scopus 로고    scopus 로고
    • Highly conserved non-coding sequences are associated with developmental control genes in vertebrates
    • Woofle A, Goodson M, Goode D, et al. Highly conserved non-coding sequences are associated with developmental control genes in vertebrates. PloS Biology 2005;3:e7.
    • (2005) PloS Biology , vol.3
    • Woofle, A.1    Goodson, M.2    Goode, D.3
  • 37
    • 33748764013 scopus 로고    scopus 로고
    • Comparative genomics at the vertebrate extremes
    • Bofelli D, Nobrega M, Rubin E. Comparative genomics at the vertebrate extremes. Nat Rev Genet 2005;6:151-57.
    • (2005) Nat Rev Genet , vol.6 , pp. 151-157
    • Bofelli, D.1    Nobrega, M.2    Rubin, E.3
  • 38
    • 13144295005 scopus 로고    scopus 로고
    • Conserved non-genic sequences - An unexpected feature of mammalian genomes
    • Dermitzakis M, Reymond A, Antonarakis S. Conserved non-genic sequences - an unexpected feature of mammalian genomes. Nat Rev Genet 2005;6:151-57.
    • (2005) Nat Rev Genet , vol.6 , pp. 151-157
    • Dermitzakis, M.1    Reymond, A.2    Antonarakis, S.3
  • 39
    • 2542542256 scopus 로고    scopus 로고
    • Ultraconserved elements in human genome
    • Bejerano G, Pheasant M, Makunin I, et al. Ultraconserved elements in human genome. Science 2004;304:1321.
    • (2004) Science , vol.304 , pp. 1321
    • Bejerano, G.1    Pheasant, M.2    Makunin, I.3
  • 40
    • 0033026626 scopus 로고    scopus 로고
    • High sequence turnover in the regulatory regions of the developmental gene hunchback in insects
    • Hancock JM, Shaw P, Bonneton F, et al. High sequence turnover in the regulatory regions of the developmental gene hunchback in insects. Mol Biol Evol 1999;16:253-65.
    • (1999) Mol Biol Evol , vol.16 , pp. 253-265
    • Hancock, J.M.1    Shaw, P.2    Bonneton, F.3
  • 41
    • 0034598832 scopus 로고    scopus 로고
    • Evidence for stabilizing selection in eukaryotic enhancer element
    • Ludwig MZ, Bergman C, Patel NH, et al. Evidence for stabilizing selection in eukaryotic enhancer element. Nature 2000;403:564-67.
    • (2000) Nature , vol.403 , pp. 564-567
    • Ludwig, M.Z.1    Bergman, C.2    Patel, N.H.3
  • 42
    • 0033858908 scopus 로고    scopus 로고
    • Evolution of transcriptional regulation
    • Tautz D. Evolution of transcriptional regulation. Curr Opin Genet Dev 2000;10:575-79.
    • (2000) Curr Opin Genet Dev , vol.10 , pp. 575-579
    • Tautz, D.1
  • 43
    • 0033030389 scopus 로고    scopus 로고
    • Interpolated Markov chains for eukaryotic promoter recognition
    • Ohler U, Harbeck S, Niemann H, et al. Interpolated Markov chains for eukaryotic promoter recognition. Bioinformatics 1999;15:362-9.
    • (1999) Bioinformatics , vol.15 , pp. 362-369
    • Ohler, U.1    Harbeck, S.2    Niemann, H.3
  • 44
    • 0034065725 scopus 로고    scopus 로고
    • Promoter prediction on a genomic scale - The Adh experience
    • Ohler U. Promoter prediction on a genomic scale - the Adh experience. Genome Res 2000;10:539-42.
    • (2000) Genome Res , vol.10 , pp. 539-542
    • Ohler, U.1
  • 45
    • 0035224747 scopus 로고    scopus 로고
    • Joint modelling of DNA sequence and physical properties to improve eukaryotic promoter recognition
    • Ohler U, Niemann H, Liao G, et al. Joint modelling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics 2001;17S:199-206.
    • (2001) Bioinformatics , vol.17 S , pp. 199-206
    • Ohler, U.1    Niemann, H.2    Liao, G.3
  • 46
    • 2942517992 scopus 로고    scopus 로고
    • Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency
    • Nazina A, Papatsenko D. Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency. BMC Bioinformatics 2003;4:65-78.
    • (2003) BMC Bioinformatics , vol.4 , pp. 65-78
    • Nazina, A.1    Papatsenko, D.2
  • 47
    • 25444528967 scopus 로고    scopus 로고
    • Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in Drosophila genome: The fluffy-tail test
    • Abnizova I, te Boekhorst R, Walter K, et al. Some statistical properties of regulatory DNA sequences, and their use in predicting regulatory regions in Drosophila genome: The fluffy-tail test. BMC Bioinformatics 2005;6:1-12.
    • (2005) BMC Bioinformatics , vol.6 , pp. 1-12
    • Abnizova, I.1    te Boekhorst, R.2    Walter, K.3
  • 48
    • 0031860393 scopus 로고    scopus 로고
    • Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL
    • Heinemeyer T, Wingender E, Reuter I, et al. Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. Nucleic Acids Res 1998;26:362-67.
    • (1998) Nucleic Acids Res , vol.26 , pp. 362-367
    • Heinemeyer, T.1    Wingender, E.2    Reuter, I.3
  • 49
    • 2542584654 scopus 로고    scopus 로고
    • Detection of functional motifs via statistical representation
    • Frith M, Fu Y, Chen J, et al. Detection of functional motifs via statistical representation. Nucleic Acid Res 2004;32: 1372-81.
    • (2004) Nucleic Acid Res , vol.32 , pp. 1372-1381
    • Frith, M.1    Fu, Y.2    Chen, J.3
  • 50
    • 0037396807 scopus 로고    scopus 로고
    • Computationally identifying novel NF-kappa B-regulated immune genes in the human genome
    • Liu R, McEachin R, States D. Computationally identifying novel NF-kappa B-regulated immune genes in the human genome. Genome Res 2003;13:654-8.
    • (2003) Genome Res , vol.13 , pp. 654-658
    • Liu, R.1    McEachin, R.2    States, D.3
  • 51
    • 0037386472 scopus 로고    scopus 로고
    • An approach to identify over-represented cis-elements in related sequences
    • Zheng J, Wu J, Sun Z. An approach to identify over-represented cis-elements in related sequences. Nucleic Acid Res 2003;31:1995-2005.
    • (2003) Nucleic Acid Res , vol.31 , pp. 1995-2005
    • Zheng, J.1    Wu, J.2    Sun, Z.3
  • 52
    • 0032483307 scopus 로고    scopus 로고
    • Extracting regulatory sites from the upstream regions of yeast genes by computational analysis of oligonucleotide frequencies
    • van Helden J, Andre B, Collado-Vides J. Extracting regulatory sites from the upstream regions of yeast genes by computational analysis of oligonucleotide frequencies. J Mol Biol 1998;281:827-42.
    • (1998) J Mol Biol , vol.281 , pp. 827-842
    • van Helden, J.1    Andre, B.2    Collado-Vides, J.3
  • 53
    • 0034656326 scopus 로고    scopus 로고
    • Discovering regulatory elements in non coding sequences by analysis of spaced dyads
    • van Helden J, Rios A, Collado-Vides J. Discovering regulatory elements in non coding sequences by analysis of spaced dyads. Nucleic Acid Res 2000;28:1808-18.
    • (2000) Nucleic Acid Res , vol.28 , pp. 1808-1818
    • van Helden, J.1    Rios, A.2    Collado-Vides, J.3
  • 54
    • 0033289316 scopus 로고    scopus 로고
    • An exact method for finding short motifs in sequences, with application to the ribosome binding site problem
    • In Heidelberg, Germany
    • Tompa M. An exact method for finding short motifs in sequences, with application to the ribosome binding site problem. In Proceedings of the 7th Int. Conf. On Intell. Systems for Mol. Biology1999, 262-71, Heidelberg, Germany.
    • (1999) Proceedings of the 7th Int. Conf. On Intell. Systems for Mol. Biology , pp. 262-271
    • Tompa, M.1
  • 55
    • 0032413411 scopus 로고    scopus 로고
    • Pedicting gene regulatory elements in silico on a genomic scale
    • Brazma A, Jonassen I, Vilo J, et al. Pedicting gene regulatory elements in silico on a genomic scale. Genome Res 1998;8: 1202-15.
    • (1998) Genome Res , vol.8 , pp. 1202-1215
    • Brazma, A.1    Jonassen, I.2    Vilo, J.3
  • 56
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • Herts GS, Stormo G. Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999;15:563-77.
    • (1999) Bioinformatics , vol.15 , pp. 563-577
    • Herts, G.S.1    Stormo, G.2
  • 57
    • 0033028596 scopus 로고    scopus 로고
    • Systematic determination of genetic network architecture
    • Tavazoie S, Hughes J, Campbell M, et al. Systematic determination of genetic network architecture. Nature Genetics 1999;22:281-85.
    • (1999) Nature Genetics , vol.22 , pp. 281-285
    • Tavazoie, S.1    Hughes, J.2    Campbell, M.3
  • 58
    • 0032561246 scopus 로고    scopus 로고
    • The transcriptional programm of sporulation in budding yeast
    • Chu S, DeRisi J, Eisen M, et al. The transcriptional programm of sporulation in budding yeast. Science 2001; 282:699-705.
    • (2001) Science , vol.282 , pp. 699-705
    • Chu, S.1    DeRisi, J.2    Eisen, M.3
  • 59
    • 0035999971 scopus 로고    scopus 로고
    • Distribution patterns of over-represented k-mers in non coding yeast genome
    • Hampson S, Kibler S, Baldi P. Distribution patterns of over-represented k-mers in non coding yeast genome. Bioiformatics 2002;18:513-28.
    • (2002) Bioiformatics , vol.18 , pp. 513-528
    • Hampson, S.1    Kibler, S.2    Baldi, P.3
  • 60
    • 0033677426 scopus 로고    scopus 로고
    • Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification
    • Marsan L, Sagot M. Algorithms for extracting structured motifs using a suffix tree with application to promoter and regulatory site consensus identification. J Comput Biol 2000; 7:345-60.
    • (2000) J Comput Biol , vol.7 , pp. 345-360
    • Marsan, L.1    Sagot, M.2
  • 61
    • 0036107903 scopus 로고    scopus 로고
    • Discovery of regulatory elements by a computational method for phylogenetic footprinting
    • Blanchette M, Tompa M. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Research 2002;12(5):739-48.
    • (2002) Genome Research , vol.12 , Issue.5 , pp. 739-748
    • Blanchette, M.1    Tompa, M.2
  • 63
    • 0042561796 scopus 로고    scopus 로고
    • Of mice and men: Phylogenetic footprinting aids the discovery of regulatory elements
    • Zhang Z, Gerstein M. Of mice and men: Phylogenetic footprinting aids the discovery of regulatory elements. J Biol 2003;2:11-17.
    • (2003) J Biol , vol.2 , pp. 11-17
    • Zhang, Z.1    Gerstein, M.2
  • 64
    • 22144491990 scopus 로고    scopus 로고
    • MONKEY: Identifying conserfed transcription factor binding sites in multiple alignments using a binding site-specific evolutionary model
    • Moses A, Chiang D, Pollard D, et al. MONKEY: Identifying conserfed transcription factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol 2004;5:R98.
    • (2004) Genome Biol , vol.5
    • Moses, A.1    Chiang, D.2    Pollard, D.3
  • 65
    • 15244358503 scopus 로고    scopus 로고
    • Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals
    • Xie X, Jun Lu, Kulbokas E, et al. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature 2005; 434:3441.
    • (2005) Nature , vol.434 , pp. 3441
    • Xie, X.1    Jun, Lu.2    Kulbokas, E.3
  • 66
    • 0034284481 scopus 로고    scopus 로고
    • Conserved non coding sequences are reliable guides to regulatory elements
    • Hardison RC. Conserved non coding sequences are reliable guides to regulatory elements. Trands Genets 2000; 16:369-72.
    • (2000) Trands Genets , vol.16 , pp. 369-372
    • Hardison, R.C.1
  • 67
    • 0142084743 scopus 로고    scopus 로고
    • Scanning human gene deserts for long-range enhancers
    • Nobrega MA, Ovcharenko I, Afzal V, et al. Scanning human gene deserts for long-range enhancers. Science 2003; 302:413.
    • (2003) Science , vol.302 , pp. 413
    • Nobrega, M.A.1    Ovcharenko, I.2    Afzal, V.3
  • 68
    • 0037249564 scopus 로고    scopus 로고
    • CORG: A database for COmparative Regulatory Genomics
    • Dieterich C, Wang H, Rateitschak K, et al. CORG: A database for COmparative Regulatory Genomics. Nucleic Acid Res 2003;31(1):55-57.
    • (2003) Nucleic Acid Res , vol.31 , Issue.1 , pp. 55-57
    • Dieterich, C.1    Wang, H.2    Rateitschak, K.3
  • 69
    • 0035986888 scopus 로고    scopus 로고
    • Evolution of transcription factor binding sites in Mammalian gene regulatory regions: Conservation and turnover
    • Dermitzakis E, Clark A. Evolution of transcription factor binding sites in Mammalian gene regulatory regions: Conservation and turnover. Mol Biol Evol 2002;19: 1114-21.
    • (2002) Mol Biol Evol , vol.19 , pp. 1114-1121
    • Dermitzakis, E.1    Clark, A.2
  • 70
    • 0037498017 scopus 로고    scopus 로고
    • Turnover of binding sites for transcription factors involved in early Drosophila development
    • Costas J, Casares F, Viera J. Turnover of binding sites for transcription factors involved in early Drosophila development. Gene 2003;310:215-20.
    • (2003) Gene , vol.310 , pp. 215-220
    • Costas, J.1    Casares, F.2    Viera, J.3
  • 71
    • 2942517986 scopus 로고    scopus 로고
    • Conservation of regulatory elements between two species of Drosophila
    • Emberly E, Rajevsky N, Siggia E. Conservation of regulatory elements between two species of Drosophila. BMC Bioinformatics 2003;4:57.
    • (2003) BMC Bioinformatics , vol.4 , pp. 57
    • Emberly, E.1    Rajevsky, N.2    Siggia, E.3
  • 72
    • 21044431735 scopus 로고    scopus 로고
    • Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution
    • Cheng J, Kapranov P, Drenkow J, et al. Transcriptional Maps of 10 Human Chromosomes at 5-Nucleotide Resolution. Science 2005;308:1149-54.
    • (2005) Science , vol.308 , pp. 1149-1154
    • Cheng, J.1    Kapranov, P.2    Drenkow, J.3
  • 73
    • 0033655171 scopus 로고    scopus 로고
    • ANN-Spec: A method for discovering transcription factor binding sites with improved specificity
    • Workman C, Stormo G. ANN-Spec: A method for discovering transcription factor binding sites with improved specificity. Pac. Symph Biocomput 2000;467-78.
    • (2000) Pac. Symph Biocomput , pp. 467-478
    • Workman, C.1    Stormo, G.2
  • 74
    • 14944363825 scopus 로고    scopus 로고
    • NestedMICA: Sensitive inference of over-represented motifs in nucleic acid sequence
    • Down T, Hubbard T. NestedMICA: Sensitive inference of over-represented motifs in nucleic acid sequence. Nucleic Acids Res 2005;33(5):1445-53.
    • (2005) Nucleic Acids Res , vol.33 , Issue.5 , pp. 1445-1453
    • Down, T.1    Hubbard, T.2
  • 75
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
    • Lawrence E, Altshul S, Boguski S, et al. Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science 1993;262:208-14.
    • (1993) Science , vol.262 , pp. 208-214
    • Lawrence, E.1    Altshul, S.2    Boguski, S.3
  • 76
    • 0002759539 scopus 로고    scopus 로고
    • Unsupervised learning of multiple motifs in biopolymers using expectation maximization
    • 1995. (MEME)
    • Bailey T, Elkan C. Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine learning 2003;21:51-80,1995. (MEME).
    • (2003) Machine Learning , vol.21 , pp. 51-80
    • Bailey, T.1    Elkan, C.2
  • 77
    • 0034730161 scopus 로고    scopus 로고
    • Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis ("MobyDick")
    • Bussemaker H, Li H, Sigia E. Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis ("MobyDick"). PNAS 2000;97(18): 10096-99.
    • (2000) PNAS , vol.97 , Issue.18 , pp. 10096-10099
    • Bussemaker, H.1    Li, H.2    Sigia, E.3
  • 78
    • 0036122720 scopus 로고    scopus 로고
    • Extraction of functional binding sites from unique regulatory regions: The Drosophila early developmental enhancers
    • Papatsenko D, Makeev V, Lifanov A, et al. Extraction of functional binding sites from unique regulatory regions: The Drosophila early developmental enhancers. Genome Res 2002;12(1):470-81.
    • (2002) Genome Res , vol.12 , Issue.1 , pp. 470-481
    • Papatsenko, D.1    Makeev, V.2    Lifanov, A.3
  • 79
    • 15744362285 scopus 로고    scopus 로고
    • Computational methods for transcriptional regulation
    • Siggia E. Computational methods for transcriptional regulation. Curr opin Genet Dev 2005;15:214-21.
    • (2005) Curr Opin Genet Dev , vol.15 , pp. 214-221
    • Siggia, E.1
  • 80
    • 22144459722 scopus 로고    scopus 로고
    • Prediction of cis-regulatory elements using binding site matrices - The success, the failures and the reasons for both
    • Vavouri T, Elgar G. Prediction of cis-regulatory elements using binding site matrices - the success, the failures and the reasons for both. Curr opin Genet Dev 2005;15:395-402.
    • (2005) Curr Opin Genet Dev , vol.15 , pp. 395-402
    • Vavouri, T.1    Elgar, G.2
  • 81
    • 1342309208 scopus 로고    scopus 로고
    • Metrics for comparing regulatory sequences on the basis of pattern counts
    • van Helden J. Metrics for comparing regulatory sequences on the basis of pattern counts. Bioinformatics 2004;20:399-406.
    • (2004) Bioinformatics , vol.20 , pp. 399-406
    • van Helden, J.1
  • 82
    • 2542584654 scopus 로고    scopus 로고
    • Detection of functional motifs via statistical representation
    • Frith M, Fu Y, Chen J, et al. Detection of functional motifs via statistical representation. Nucleic Acids Res 2004; 32:1372-81.
    • (2004) Nucleic Acids Res , vol.32 , pp. 1372-1381
    • Frith, M.1    Fu, Y.2    Chen, J.3
  • 83
    • 3242892432 scopus 로고    scopus 로고
    • Complexity: An internet resource for analysis of DNA sequence complexity
    • on-line
    • Orlov Y, Potapov V. Complexity: An internet resource for analysis of DNA sequence complexity. Nucleic Acids Res 2004;32 on-line.
    • (2004) Nucleic Acids Res , vol.32
    • Orlov, Y.1    Potapov, V.2
  • 84
    • 0037398319 scopus 로고    scopus 로고
    • Homotypic regulatory lists in Drosophila
    • Lifanov AP, Makeev VJ, Nazina AG, et al. Homotypic regulatory lists in Drosophila. Genome Res 2003;13(4): 579-88.
    • (2003) Genome Res , vol.13 , Issue.4 , pp. 579-588
    • Lifanov, A.P.1    Makeev, V.J.2    Nazina, A.G.3
  • 85
    • 4444362206 scopus 로고    scopus 로고
    • Clustering of DNA Sequences in Human Promoters
    • FitzGerald P, Shlyakhtenko A, Mir A, et al. Clustering of DNA Sequences in Human Promoters. Genome Res 2004; 14:1562-74.
    • (2004) Genome Res , vol.14 , pp. 1562-1574
    • FitzGerald, P.1    Shlyakhtenko, A.2    Mir, A.3
  • 86
    • 0037443976 scopus 로고    scopus 로고
    • Toucan: Deciphering the cis-regulatory logic of co-regulated genes
    • Aerts S, Thijs G, Coessens B, et al. Toucan: Deciphering the cis-regulatory logic of co-regulated genes. Nucleic Acids Res 2003;31:1753-64.
    • (2003) Nucleic Acids Res , vol.31 , pp. 1753-1764
    • Aerts, S.1    Thijs, G.2    Coessens, B.3
  • 87
    • 1242326890 scopus 로고    scopus 로고
    • CRÈME: A framework for identifying cis-regulatory modules in human-mouse conserved segments
    • Sharan R, Ovcharenko I, Ben-Hur A, et al. CRÈME: A framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics 2003; T19:283-91.
    • (2003) Bioinformatics , vol.T19 , pp. 283-291
    • Sharan, R.1    Ovcharenko, I.2    Ben-Hur, A.3
  • 89
    • 0035945567 scopus 로고    scopus 로고
    • Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
    • Iyer VR, Horak CE, Scafe CS, et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 2001;409:533-38.
    • (2001) Nature , vol.409 , pp. 533-538
    • Iyer, V.R.1    Horak, C.E.2    Scafe, C.S.3
  • 90
    • 0035844087 scopus 로고    scopus 로고
    • Control of a genetic regulatory network by a selector gene
    • Guss KA, Nelson CE, Hudson A, et al. Control of a genetic regulatory network by a selector gene. Science 2001;292: 1164-67.
    • (2001) Science , vol.292 , pp. 1164-1167
    • Guss, K.A.1    Nelson, C.E.2    Hudson, A.3


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