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Volumn 5, Issue 4, 2004, Pages 276-287

Applied bioinformatics for the identification of regulatory elements

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; COMPUTER PROGRAM; DNA FOOTPRINTING; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC ALGORITHM; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENOME; HUMAN; METAZOON; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; REGULATORY MECHANISM; REVIEW; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION;

EID: 1842584947     PISSN: 14710056     EISSN: None     Source Type: Journal    
DOI: 10.1038/nrg1315     Document Type: Review
Times cited : (915)

References (98)
  • 3
    • 0035999672 scopus 로고    scopus 로고
    • Analysis of mRNA expression and protein abundance data: An approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts
    • Greenbaum, D., Jansen, R. & Gerstein, M. Analysis of mRNA expression and protein abundance data: an approach for the comparison of the enrichment of features in the cellular population of proteins and transcripts. Bioinformatics 18, 585-596 (2002).
    • (2002) Bioinformatics , vol.18 , pp. 585-596
    • Greenbaum, D.1    Jansen, R.2    Gerstein, M.3
  • 4
    • 0348062819 scopus 로고    scopus 로고
    • The Eukaryotic Promoter Database EPD the impact of in silico primer extension
    • Schmid, C. D., Praz, V., Delorenzi, M., Perier, R. & Bucher, P. The Eukaryotic Promoter Database EPD: the impact of in silico primer extension. Nucleic Acids Res. 32, D82-D85 (2004).
    • (2004) Nucleic Acids Res. , vol.32
    • Schmid, C.D.1    Praz, V.2    Delorenzi, M.3    Perier, R.4    Bucher, P.5
  • 5
    • 0030863002 scopus 로고    scopus 로고
    • Eukaryotic promoter recognition
    • Fickett, J. W. & Hatzigeorgiou, A. G. Eukaryotic promoter recognition. Genome Res. 7, 861-878 (1997). Demonstrated the poor performance of promoter-prediction software. Led to a shift from predicting specific transcription start sites, and towards prediction of regions that are likely to contain a TSS.
    • (1997) Genome Res. , vol.7 , pp. 861-878
    • Fickett, J.W.1    Hatzigeorgiou, A.G.2
  • 6
    • 0025278259 scopus 로고
    • Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences
    • Bucher, P. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 212, 563-578 (1990).
    • (1990) J. Mol. Biol. , vol.212 , pp. 563-578
    • Bucher, P.1
  • 7
    • 0042329754 scopus 로고    scopus 로고
    • Structure, function and evolution of CpG island promoters
    • Antequera, F. Structure, function and evolution of CpG island promoters. Cell. Mol. Life Sci. 60, 1647-1658 (2003).
    • (2003) Cell. Mol. Life Sci. , vol.60 , pp. 1647-1658
    • Antequera, F.1
  • 8
    • 0035236049 scopus 로고    scopus 로고
    • Promoter prediction in the human genome
    • Hannenhalli, S. & Levy, S. Promoter prediction in the human genome. Bioinformatics 17 (Suppl. 1), S90-S96 (2001).
    • (2001) Bioinformatics , vol.17 , Issue.SUPPL. 1
    • Hannenhalli, S.1    Levy, S.2
  • 9
    • 0036123111 scopus 로고    scopus 로고
    • Computational detection and location of transcription start sites in mammalian genomic DNA
    • Down, T. A. & Hubbard, T. J. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res. 12, 458-461 (2002).
    • (2002) Genome Res. , vol.12 , pp. 458-461
    • Down, T.A.1    Hubbard, T.J.2
  • 10
    • 0035735265 scopus 로고    scopus 로고
    • Computational identification of promoters and first exons in the human genome
    • Davuluri, R. V., Grosse, I. & Zhang, M. Q. Computational identification of promoters and first exons in the human genome. Nature Genet. 29, 412-417 (2001).
    • (2001) Nature Genet. , vol.29 , pp. 412-417
    • Davuluri, R.V.1    Grosse, I.2    Zhang, M.Q.3
  • 11
    • 0037188910 scopus 로고    scopus 로고
    • Bidirectional gene organization: A common architectural feature of the human genome
    • Adachi, N. & Lieber, M. R. Bidirectional gene organization: a common architectural feature of the human genome. Cell 109, 807-809 (2002).
    • (2002) Cell , vol.109 , pp. 807-809
    • Adachi, N.1    Lieber, M.R.2
  • 12
    • 0023216891 scopus 로고
    • CpG islands in vertebrate genomes
    • Gardiner-Garden, M. & Frommer, M. CpG islands in vertebrate genomes. J. Mol. Biol. 196, 261-282 (1987).
    • (1987) J. Mol. Biol. , vol.196 , pp. 261-282
    • Gardiner-Garden, M.1    Frommer, M.2
  • 13
    • 0142104045 scopus 로고    scopus 로고
    • Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs
    • Okazaki, Y. et al. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420, 563-573 (2002).
    • (2002) Nature , vol.420 , pp. 563-573
    • Okazaki, Y.1
  • 14
    • 0037250168 scopus 로고    scopus 로고
    • The UCSC Genome Browser Database
    • Karolchik, D. et al. The UCSC Genome Browser Database. Nucleic Acids Res. 31, 51-64 (2003).
    • (2003) Nucleic Acids Res. , vol.31 , pp. 51-64
    • Karolchik, D.1
  • 15
    • 0036124446 scopus 로고    scopus 로고
    • Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling
    • Liu, R. & States, D. J. Consensus promoter identification in the human genome utilizing expressed gene markers and gene modeling. Genome Res. 12, 462-469 (2002).
    • (2002) Genome Res. , vol.12 , pp. 462-469
    • Liu, R.1    States, D.J.2
  • 16
    • 0347756647 scopus 로고    scopus 로고
    • DBTSS DataBase of Transcriptional Start Sites: Progress report 2004
    • Suzuki, Y., Yamashita, R., Sugano, S. & Nakai, K. DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res. 32, D78-D81 (2004).
    • (2004) Nucleic Acids Res. , vol.32
    • Suzuki, Y.1    Yamashita, R.2    Sugano, S.3    Nakai, K.4
  • 17
    • 9144233601 scopus 로고    scopus 로고
    • Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage
    • Shiraki, T. et al. Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc. Natl Acad. Sci. USA (2003). Introduces a new method for the identification of TSS on the basis of improved laboratory methods for the generation of full-length cDNAs. The data generated from this method will be important for the identification of alternative promoters.
    • (2003) Proc. Natl. Acad. Sci. USA
    • Shiraki, T.1
  • 18
    • 0037380723 scopus 로고    scopus 로고
    • Comparative genomics: Genome-wide analysis in metazoan eukaryotes
    • Ureta-Vidal, A., Ettwiller, L. & Birney, E. Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nature Rev. Genet. 4, 251-262 (2003).
    • (2003) Nature Rev. Genet. , vol.4 , pp. 251-262
    • Ureta-Vidal, A.1    Ettwiller, L.2    Birney, E.3
  • 19
    • 0037271322 scopus 로고    scopus 로고
    • Cross-species sequence comparisons: A review of methods and available resources
    • Frazer, K. A., Elnitski, L., Church, D. M., Dubchak, I. & Hardison, R. C. Cross-species sequence comparisons: a review of methods and available resources. Genome Res. 13, 1-12 (2003).
    • (2003) Genome Res. , vol.13 , pp. 1-12
    • Frazer, K.A.1    Elnitski, L.2    Church, D.M.3    Dubchak, I.4    Hardison, R.C.5
  • 20
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature 409, 860-921 (2001).
    • (2001) Nature , vol.409 , pp. 860-921
  • 21
    • 1542563409 scopus 로고    scopus 로고
    • Initial sequencing and comparative analysis of the mouse genome
    • Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420, 520-562 (2002).
    • (2002) Nature , vol.420 , pp. 520-562
  • 22
    • 0037162885 scopus 로고    scopus 로고
    • Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes
    • Aparicio, S. et al. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297, 1301-1310 (2002).
    • (2002) Science , vol.297 , pp. 1301-1310
    • Aparicio, S.1
  • 23
    • 0032509302 scopus 로고    scopus 로고
    • Genome sequence of the nematode C. elegans: A platform for investigating biology
    • C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012-2018 (1998).
    • (1998) Science , vol.282 , pp. 2012-2018
  • 24
    • 0034708480 scopus 로고    scopus 로고
    • The genome sequence of Drosophila melanogaster
    • Adams, M. D. et al. The genome sequence of Drosophila melanogaster. Science 287, 2185-2195 (2000).
    • (2000) Science , vol.287 , pp. 2185-2195
    • Adams, M.D.1
  • 25
    • 0036707816 scopus 로고    scopus 로고
    • Identification of transcription factor binding sites in the human genome sequence
    • Levy, S. & Hannenhalli, S. Identification of transcription factor binding sites in the human genome sequence. Mamm. Genome 13, 510-514 (2002).
    • (2002) Mamm. Genome , vol.13 , pp. 510-514
    • Levy, S.1    Hannenhalli, S.2
  • 26
    • 0041903634 scopus 로고    scopus 로고
    • Identification of conserved regulatory elements by comparative genome analysis
    • Lenhard, B. et al. Identification of conserved regulatory elements by comparative genome analysis. J. Biol. 2, 13 (2003). Demonstrates that phylogenetic footprinting can eliminate an order of magnitude of false-positive transcription-factor binding-site predictions, in exchange for a modest sensitivity decrease.
    • (2003) J. Biol. , vol.2 , pp. 13
    • Lenhard, B.1
  • 27
    • 0034756824 scopus 로고    scopus 로고
    • Comparative genomics of the SOX9 region in human and Fugu rubripes: Conservation of short regulatory sequence elements within large intergenic regions
    • Bagheri-Fam, S., Ferraz, C., Demaille, J., Scherer, G. & Pfeifer, D. Comparative genomics of the SOX9 region in human and Fugu rubripes: conservation of short regulatory sequence elements within large intergenic regions. Genomics 78, 73-82 (2001).
    • (2001) Genomics , vol.78 , pp. 73-82
    • Bagheri-Fam, S.1    Ferraz, C.2    Demaille, J.3    Scherer, G.4    Pfeifer, D.5
  • 28
    • 0028962333 scopus 로고
    • Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes
    • Aparicio, S. et al. Detecting conserved regulatory elements with the model genome of the Japanese puffer fish, Fugu rubripes. Proc. Natl Acad. Sci. USA 92, 1684-1688 (1995).
    • (1995) Proc. Natl. Acad. Sci. USA , vol.92 , pp. 1684-1688
    • Aparicio, S.1
  • 29
    • 0038817801 scopus 로고    scopus 로고
    • Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters
    • Santini, S., Boore, J. L. & Meyer, A. Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters. Genome Res. 18, 1111-1122 (2003).
    • (2003) Genome Res. , vol.18 , pp. 1111-1122
    • Santini, S.1    Boore, J.L.2    Meyer, A.3
  • 30
    • 0042902833 scopus 로고    scopus 로고
    • The COG database: An updated version includes eukaryotes
    • Tatusov, R. L. et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4, 41 (2003).
    • (2003) BMC Bioinformatics , vol.4 , pp. 41
    • Tatusov, R.L.1
  • 31
    • 0142028973 scopus 로고    scopus 로고
    • Comprehensive analysis of orthologous protein domains using the HOPS database
    • Storm, C. E. & Sonnhammer, E. L. Comprehensive analysis of orthologous protein domains using the HOPS database. Genome Res. 13, 2353-2362 (2003).
    • (2003) Genome Res. , vol.13 , pp. 2353-2362
    • Storm, C.E.1    Sonnhammer, E.L.2
  • 32
    • 9144233525 scopus 로고    scopus 로고
    • Database resources of the National Center for Biotechnology Information: Update
    • Wheeler, D. L. et al. Database resources of the National Center for Biotechnology Information: update. Nucleic Acids Res. 32, D35-D40 (2004).
    • (2004) Nucleic Acids Res. , vol.32
    • Wheeler, D.L.1
  • 33
    • 0037267806 scopus 로고    scopus 로고
    • Human-mouse alignments with BLASTZ
    • Schwartz, S. et al. Human-mouse alignments with BLASTZ. Genome Res. 13, 103-107 (2003).
    • (2003) Genome Res. , vol.13 , pp. 103-107
    • Schwartz, S.1
  • 34
    • 0037398368 scopus 로고    scopus 로고
    • LAGAN and Multi-LAGAN: Efficient tools for large-scale multiple alignment of genomic DNA
    • Brudno, M. et al. LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA. Genome Res. 13, 721-731 (2003). One of the best progressive alignment algorithms for global genome sequence alignment that facilitates phylogenetic footprinting.
    • (2003) Genome Res. , vol.13 , pp. 721-731
    • Brudno, M.1
  • 35
    • 0014757386 scopus 로고
    • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    • Needleman, S. B. & Wunsch, C. D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48, 443-453 (1970).
    • (1970) J. Mol. Biol. , vol.48 , pp. 443-453
    • Needleman, S.B.1    Wunsch, C.D.2
  • 36
    • 4944262040 scopus 로고    scopus 로고
    • Glocal alignment: Finding rearrangements during alignment
    • Brudno, M. et al. Glocal alignment: finding rearrangements during alignment. Bioinformatics 19 (Suppl. 1), L54-162 (2003).
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Brudno, M.1
  • 37
    • 0036105591 scopus 로고    scopus 로고
    • rVista for comparative sequence-based discovery of functional transcription factor binding sites
    • Loots, G. G., Ovcharenko, I., Pachter, L., Dubchak, I. & Rubin, E. M. rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res. 12, 832-839 (2002).
    • (2002) Genome Res. , vol.12 , pp. 832-839
    • Loots, G.G.1    Ovcharenko, I.2    Pachter, L.3    Dubchak, I.4    Rubin, E.M.5
  • 38
    • 0036935568 scopus 로고    scopus 로고
    • Pip Tools: A computational toolkit to annotate and analyze pairwise comparisons of genomic sequences
    • Elnitski, L. et al. Pip Tools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences. Genomics 80, 681-690 (2002).
    • (2002) Genomics , vol.80 , pp. 681-690
    • Elnitski, L.1
  • 39
    • 18344415808 scopus 로고    scopus 로고
    • Distinguishing regulatory DNA from neutral sites
    • Elnitski, L. et al. Distinguishing regulatory DNA from neutral sites. Genome Res. 13, 64-72 (2003). A new method to classify functions of conserved regions as regulatory or coding on the basis of the pattern of identical nucleotides.
    • (2003) Genome Res. , vol.13 , pp. 64-72
    • Elnitski, L.1
  • 40
    • 0041465867 scopus 로고    scopus 로고
    • Comparative analyses of multi-species sequences from targeted genomic regions
    • Thomas, J. W. et al. Comparative analyses of multi-species sequences from targeted genomic regions. Nature 424, 788-793 (2003). A first look at methods to analyse large sets of orthologous eukaryotic gene sequences.
    • (2003) Nature , vol.424 , pp. 788-793
    • Thomas, J.W.1
  • 41
    • 2442673974 scopus 로고    scopus 로고
    • Sockeye: A 3D environment for comparative genomics
    • in the press
    • Montgomery, S. B. et al. Sockeye: A 3D environment for comparative genomics. Genome Res. (in the press).
    • Genome Res.
    • Montgomery, S.B.1
  • 42
    • 0036500609 scopus 로고    scopus 로고
    • A genomic regulatory network for development
    • Davidson, E. H. et al. A genomic regulatory network for development. Science 295, 1669-1678 (2002). One of several papers by Davidson that constructs the argument that genes are regulated by composite interactions of transcription factors that interact with locally dense clusters of binding sites.
    • (2002) Science , vol.295 , pp. 1669-1678
    • Davidson, E.H.1
  • 43
    • 0141730403 scopus 로고    scopus 로고
    • The β-globin nuclear compartment in development and erythroid differentiation
    • Palstra, R. J. et al. The β-globin nuclear compartment in development and erythroid differentiation. Nature Genet. 35, 190-194 (2003).
    • (2003) Nature Genet. , vol.35 , pp. 190-194
    • Palstra, R.J.1
  • 44
    • 0029655429 scopus 로고    scopus 로고
    • Quantitative discrimination of MEF2 sites
    • Fickett, J. W. Quantitative discrimination of MEF2 sites. Mol. Cell Biol. 16, 437-441 (1996).
    • (1996) Mol. Cell Biol. , vol.16 , pp. 437-441
    • Fickett, J.W.1
  • 45
    • 0029935832 scopus 로고    scopus 로고
    • Coordinate positioning of MEF2 and myogenin binding sites
    • Fickett, J. W. Coordinate positioning of MEF2 and myogenin binding sites. Gene 172, GC19-GC32 (1996).
    • (1996) Gene , vol.172
    • Fickett, J.W.1
  • 46
    • 0031581855 scopus 로고    scopus 로고
    • Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome
    • Tronche, F., Ringeisen, F., Blumenfeld, M., Yaniv, M. & Pontoglio, M. Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J. Mol. Biol. 266, 231-245 (1997). Demonstration that matrix-based profiles for the prediction of transcription-factor binding sites accurately predict in vitro binding.
    • (1997) J. Mol. Biol. , vol.266 , pp. 231-245
    • Tronche, F.1    Ringeisen, F.2    Blumenfeld, M.3    Yaniv, M.4    Pontoglio, M.5
  • 47
    • 0025187297 scopus 로고
    • A sensitive method for the determination of protein-DNA binding specificities
    • Pollock, R. & Treisman, R. A sensitive method for the determination of protein-DNA binding specificities. Nucleic Acids Res. 18, 6197-6204 (1990).
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6197-6204
    • Pollock, R.1    Treisman, R.2
  • 48
    • 0033028741 scopus 로고    scopus 로고
    • Quantifying DNA-protein interactions by double-stranded DNA arrays
    • Bulyk, M. L., Gentalen, E., Lockhart, D. J. & Church, G. M. Quantifying DNA-protein interactions by double-stranded DNA arrays. Nature Biotechnol. 17, 573-577 (1999).
    • (1999) Nature Biotechnol. , vol.17 , pp. 573-577
    • Bulyk, M.L.1    Gentalen, E.2    Lockhart, D.J.3    Church, G.M.4
  • 49
    • 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, R. K. & Schneider, T. D. 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).
    • (1999) Nucleic Acids Res. , vol.27 , pp. 882-887
    • Shultzaberger, R.K.1    Schneider, T.D.2
  • 50
    • 0036022523 scopus 로고    scopus 로고
    • High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites
    • Roulet, E. et al. High-throughput SELEX SAGE method for quantitative modeling of transcription-factor binding sites. Nature Biotechnol. 20, 831-835 (2002).
    • (2002) Nature Biotechnol. , vol.20 , pp. 831-835
    • Roulet, E.1
  • 51
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: Representation and discovery
    • Stormo, G. D. DNA binding sites: representation and discovery. Bioinformatics 16, 16-23 (2000). An excellent explanation of the relationship between scores that are produced by binding-site profiles and binding energy.
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 52
    • 0141974916 scopus 로고    scopus 로고
    • A non-parametric model for transcription factor binding sites
    • King, O. D. & Roth, F. P. A non-parametric model for transcription factor binding sites. Nucleic Acids Res. 31, e116 (2003).
    • (2003) Nucleic Acids Res. , vol.31
    • King, O.D.1    Roth, F.P.2
  • 53
    • 0023147228 scopus 로고
    • Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters
    • Berg, O. G. & von Hippel, P. H. Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol. 193, 723-750 (1987).
    • (1987) J. Mol. Biol. , vol.193 , pp. 723-750
    • Berg, O.G.1    Von Hippel, P.H.2
  • 56
    • 0037109192 scopus 로고    scopus 로고
    • Additivity in protein-DNA interactions: How good an approximation is it?
    • Benos, P. V., Bulyk, M. L. & Stormo, G. D. Additivity in protein-DNA interactions: how good an approximation is it? Nucleic Acids Res. 30, 4442-4451 (2002). Summary of several key papers that demonstrate that matrix profiles provide reasonable predictions of binding sites in most cases.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 4442-4451
    • Benos, P.V.1    Bulyk, M.L.2    Stormo, G.D.3
  • 57
    • 0034086140 scopus 로고    scopus 로고
    • Origins and evolutionary diversification of the nuclear receptor superfamily
    • Owen, G. I. & Zelent, A. Origins and evolutionary diversification of the nuclear receptor superfamily. Cell. Mol. Life Sci. 67, 809-827 (2000).
    • (2000) Cell. Mol. Life Sci. , vol.67 , pp. 809-827
    • Owen, G.I.1    Zelent, A.2
  • 58
    • 0034615781 scopus 로고    scopus 로고
    • Experimental analysis and computer prediction of CTF/NFJ transcription factor DNA binding sites
    • Roulet, E. et al. Experimental analysis and computer prediction of CTF/NFJ transcription factor DNA binding sites. J. Mol. Biol. 297, 833-848 (2000).
    • (2000) J. Mol. Biol. , vol.297 , pp. 833-848
    • Roulet, E.1
  • 59
  • 60
    • 0037270315 scopus 로고    scopus 로고
    • AVID: A global alignment program
    • Bray, N., Dubchak, I. & Pachter, L. AVID: a global alignment program. Genome Res. 13, 97-102 (2003).
    • (2003) Genome Res. , vol.13 , pp. 97-102
    • Bray, N.1    Dubchak, I.2    Pachter, L.3
  • 61
    • 0037208166 scopus 로고    scopus 로고
    • TRANSFAC: Transcriptional regulation, from patterns to profiles
    • Matys, V. et al. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31, 374-378 (2003).
    • (2003) Nucleic Acids Res. , vol.31 , pp. 374-378
    • Matys, V.1
  • 62
    • 0036677662 scopus 로고    scopus 로고
    • TFBS: Computational framework for transcription factor binding site analysis
    • Lenhard, B. & Wasserman, W. W. TFBS: computational framework for transcription factor binding site analysis. Bioinformatics 18, 1135-1136 (2002).
    • (2002) Bioinformatics , vol.18 , pp. 1135-1136
    • Lenhard, B.1    Wasserman, W.W.2
  • 63
    • 0035986888 scopus 로고    scopus 로고
    • Evolution of transcription factor binding sites in mammalian gene regulatory regions: Conservation and turnover
    • Dermitzakis, E. T. & Clark, A. G. Evolution of transcription factor binding sites in mammalian gene regulatory regions: conservation and turnover. Mol. Biol. Evol. 19, 1114-1121 (2002).
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1114-1121
    • Dermitzakis, E.T.1    Clark, A.G.2
  • 64
    • 0042697343 scopus 로고    scopus 로고
    • The evolution of transcriptional regulation in eukaryotes
    • Wray, G. A. et al. The evolution of transcriptional regulation in eukaryotes. Mol. Biol. Evol. 20, 1377-1419 (2003). An examination of the patterns of sequence evolution in regulatory regions. Surveys the genetic consequences of changes in binding sites.
    • (2003) Mol. Biol. Evol. , vol.20 , pp. 1377-1419
    • Wray, G.A.1
  • 65
    • 0023821768 scopus 로고
    • Embryonic ε- and γ-globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints
    • Tagle, D. A. et al. Embryonic ε- and γ-globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J. Mol. Biol. 203, 439-455 (1988). One of several papers from the group that, to the best of our knowledge, established the phrase 'phylogenetic footprinting'.
    • (1988) J. Mol. Biol. , vol.203 , pp. 439-455
    • Tagle, D.A.1
  • 66
    • 0242418246 scopus 로고    scopus 로고
    • Phylogenetic shadowing of primate sequences to find functional regions of the human genome
    • Boffelli, D. et al. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299, 1391-1394 (2003).
    • (2003) Science , vol.299 , pp. 1391-1394
    • Boffelli, D.1
  • 67
    • 0032562789 scopus 로고    scopus 로고
    • Identification of regulatory regions which confer muscle-specific gene expression
    • Wasserman, W. W. & Fickett, J. W. Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol. 278, 167-181 (1998).
    • (1998) J. Mol. Biol. , vol.278 , pp. 167-181
    • Wasserman, W.W.1    Fickett, J.W.2
  • 68
    • 0042121118 scopus 로고    scopus 로고
    • Cluster-Buster: Finding dense clusters of motifs in DNA sequences
    • Frith, M. C., Li, M. C. & Weng, Z. Cluster-Buster: finding dense clusters of motifs in DNA sequences. Nucleic Acids Res. 31, 3666-3668 (2003).
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3666-3668
    • Frith, M.C.1    Li, M.C.2    Weng, Z.3
  • 69
    • 0034819935 scopus 로고    scopus 로고
    • A predictive model for regulatory sequences directing liver-specific transcription
    • Krivan, W. & Wasserman, W. W. A predictive model for regulatory sequences directing liver-specific transcription. Genome Res. 11, 1559-1566 (2001). Demonstration that coupling module predictions with phylogenetic footprinting can result in reliable predictions of regulatory sequences.
    • (2001) Genome Res. , vol.11 , pp. 1559-1566
    • Krivan, W.1    Wasserman, W.W.2
  • 70
    • 0037396807 scopus 로고    scopus 로고
    • Computationally identifying novel NF-κ B-regulated immune genes in the human genome
    • Liu, R., McEachin, R. C. & States, D. J. Computationally identifying novel NF-κ B-regulated immune genes in the human genome. Genome Res. 13, 654-661 (2003).
    • (2003) Genome Res. , vol.13 , pp. 654-661
    • Liu, R.1    McEachin, R.C.2    States, D.J.3
  • 71
    • 0037154273 scopus 로고    scopus 로고
    • Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome
    • Berman, B. P. et al. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl Acad. Sci. USA 99, 757-762 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 757-762
    • Berman, B.P.1
  • 72
    • 0041389077 scopus 로고    scopus 로고
    • Identification of functional clusters of transcription factor binding motifs in genome sequences: The MSCAN algorithm
    • Johansson, O., Alkema, W., Wasserman, W. W. & Lagergren, J. Identification of functional clusters of transcription factor binding motifs in genome sequences: the MSCAN algorithm. Bioinformatics 19 (Suppl. 1), I169-I176 (2003).
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Johansson, O.1    Alkema, W.2    Wasserman, W.W.3    Lagergren, J.4
  • 73
    • 4043156577 scopus 로고    scopus 로고
    • Searching for statistically significant regulatory modules
    • Bailey, T. L. & Noble, W. S. Searching for statistically significant regulatory modules. Bioinformatics 19 (Suppl. 2), II16-II25 (2003).
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 2
    • Bailey, T.L.1    Noble, W.S.2
  • 74
  • 75
    • 2942576308 scopus 로고    scopus 로고
    • Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo
    • Rajewsky, N., Vergassola, M., Gaul, U. & Siggia, E. D. Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics 3, 30 (2002). An excellent algorithm for the detection of locally dense clusters of transcription-factor binding sites, particularly orientated towards large clusters of sites for a single factor.
    • (2002) BMC Bioinformatics , vol.3 , pp. 30
    • Rajewsky, N.1    Vergassola, M.2    Gaul, U.3    Siggia, E.D.4
  • 77
    • 85080847134 scopus 로고    scopus 로고
    • Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics
    • in the press
    • Sandelin, A. & Wasserman, W. W. Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J. Mol. Biol. (in the press).
    • J. Mol. Biol.
    • Sandelin, A.1    Wasserman, W.W.2
  • 79
    • 0038724989 scopus 로고    scopus 로고
    • Finding functional features in Saccharomyces genomes by phylogenetic footprinting
    • Cliften, P. et al. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301, 71-76 (2003).
    • (2003) Science , vol.301 , pp. 71-76
    • Cliften, P.1
  • 80
    • 0037443976 scopus 로고    scopus 로고
    • Toucan: Deciphering the cis-regulatory logic of coregulated genes
    • Aerts, S. et al. Toucan: deciphering the cis-regulatory logic of coregulated genes. Nucleic Acids Res. 31, 1753-1764 (2003).
    • (2003) Nucleic Acids Res. , vol.31 , pp. 1753-1764
    • Aerts, S.1
  • 81
    • 0142074896 scopus 로고    scopus 로고
    • PAINT: A promoter analysis and interaction network generation tool for gene regulatory network identification
    • Vadigepalli, R., Chakravarthula, P., Zak, D. E., Schwaber, J. S. & Gonye, G. E. PAINT: A promoter analysis and interaction network generation tool for gene regulatory network identification. Omics 7, 235-252 (2003).
    • (2003) Omics , vol.7 , pp. 235-252
    • Vadigepalli, R.1    Chakravarthula, P.2    Zak, D.E.3    Schwaber, J.S.4    Gonye, G.E.5
  • 82
    • 0032948782 scopus 로고    scopus 로고
    • Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity
    • Klingenhoff, A., Frech, K., Quandt, K. & Werner, T. Functional promoter modules can be detected by formal models independent of overall nucleotide sequence similarity. Bioinformatics 15, 180-186 (1999).
    • (1999) Bioinformatics , vol.15 , pp. 180-186
    • Klingenhoff, A.1    Frech, K.2    Quandt, K.3    Werner, T.4
  • 83
    • 0345874725 scopus 로고    scopus 로고
    • CONREAL: Conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylo genetic footprinting
    • Berezikov, E., Guryev, V., Plasterk, R. H. & Cuppen, E. CONREAL: conserved regulatory elements anchored alignment algorithm for identification of transcription factor binding sites by phylogenetic footprinting. Genome Res. 14, 170-178 (2004).
    • (2004) Genome Res. , vol.14 , pp. 170-178
    • Berezikov, E.1    Guryev, V.2    Plasterk, R.H.3    Cuppen, E.4
  • 84
    • 0036365401 scopus 로고    scopus 로고
    • Automatic annotation of genomic regulatory sequences by searching for composite clusters
    • Kel-Margoulis, O. V., Ivanova, T. G., Wingender, E. & Kel, A. E. Automatic annotation of genomic regulatory sequences by searching for composite clusters. Pac. Symp. Biocomput. 187-198 (2002).
    • (2002) Pac. Symp. Biocomput. , pp. 187-198
    • Kel-Margoulis, O.V.1    Ivanova, T.G.2    Wingender, E.3    Kel, A.E.4
  • 85
    • 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. & Karp, R. M. CRÈME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics 19 (Suppl. 1), 1283-1291 (2003).
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1 , pp. 1283-1291
    • Sharan, R.1    Ovcharenko, I.2    Ben-Hur, A.3    Karp, R.M.4
  • 86
    • 0037438345 scopus 로고    scopus 로고
    • Quantitative approaches to problems of eukaryotic gene expression
    • Felsenfeld, G. Quantitative approaches to problems of eukaryotic gene expression. Biophys. Chem. 100, 607-613 (2003).
    • (2003) Biophys. Chem. , vol.100 , pp. 607-613
    • Felsenfeld, G.1
  • 87
    • 0038375002 scopus 로고    scopus 로고
    • Genome function and nuclear architecture: From gene expression to nanoscience
    • O'Brien, T. P. et al. Genome function and nuclear architecture: from gene expression to nanoscience. Genome Res. 13, 1029-1241 (2003).
    • (2003) Genome Res. , vol.13 , pp. 1029-1241
    • O'Brien, T.P.1
  • 88
    • 0035182436 scopus 로고    scopus 로고
    • Nucleosome formation potential of eukaryotic DNA: Calculation and promoters analysis
    • Levitsky, V. G., Podkolodnaya, O. A., Kolchanov, N. A. & Podkolodny, N. L. Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis. Bioinformatics 17, 998-1010 (2001).
    • (2001) Bioinformatics , vol.17 , pp. 998-1010
    • Levitsky, V.G.1    Podkolodnaya, O.A.2    Kolchanov, N.A.3    Podkolodny, N.L.4
  • 89
    • 0037177567 scopus 로고    scopus 로고
    • Transcription: Of chips and ChIPs
    • Shannon, M. F. & Rao, S. Transcription: of chips and ChIPs. Science 296, 666-669 (2002).
    • (2002) Science , vol.296 , pp. 666-669
    • Shannon, M.F.1    Rao, S.2
  • 90
    • 0035671406 scopus 로고    scopus 로고
    • Chromatin insulators and boundaries: Effects on transcription and nuclear organization
    • Gerasimova, T. I. & Corces, V. G. Chromatin insulators and boundaries: effects on transcription and nuclear organization. Annu. Rev. Genet, 35, 193-208 (2001).
    • (2001) Annu. Rev. Genet. , vol.35 , pp. 193-208
    • Gerasimova, T.I.1    Corces, V.G.2
  • 91
    • 0036467996 scopus 로고    scopus 로고
    • Insulators: Many functions, many mechanisms
    • West, A. G., Gaszner, M. & Felsenfeld, G. Insulators: many functions, many mechanisms. Genes Dev. 16, 271-288 (2002).
    • (2002) Genes Dev. , vol.16 , pp. 271-288
    • West, A.G.1    Gaszner, M.2    Felsenfeld, G.3
  • 92
    • 0025008168 scopus 로고
    • Sequence logos: A new way to display consensus sequences
    • Schneider, T. D. & Stephens, R. M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 18, 6097-6100 (1990).
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 93
    • 0027527487 scopus 로고
    • Regulation of the human cardiac/slow-twitch troponin C gene by multiple, cooperative, cell-type-specific, and MyoD-responsive elements
    • Christensen, T. H., Prentice, H., Gahlmann, R. & Kedes, L. Regulation of the human cardiac/slow-twitch troponin C gene by multiple, cooperative, cell-type-specific, and MyoD-responsive elements. Mol. Cell Biol. 13, 6752-6765 (1993).
    • (1993) Mol. Cell Biol. , vol.13 , pp. 6752-6765
    • Christensen, T.H.1    Prentice, H.2    Gahlmann, R.3    Kedes, L.4
  • 94
    • 0028153479 scopus 로고
    • A novel myogenic regulatory circuit controls slow/cardiac troponin C gene transcription in skeletal muscle
    • Parmacek, M. S. et al. A novel myogenic regulatory circuit controls slow/cardiac troponin C gene transcription in skeletal muscle. Mol. Cell Biol. 14, 1870-1885 (1994).
    • (1994) Mol. Cell Biol. , vol.14 , pp. 1870-1885
    • Parmacek, M.S.1
  • 95
    • 0041853625 scopus 로고    scopus 로고
    • MATCH: A tool for searching transcription factor binding sites in DNA sequences
    • Kel, A. E. et al. MATCH: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res. 31, 3576-3579 (2003).
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3576-3579
    • Kel, A.E.1
  • 96
    • 0037246585 scopus 로고    scopus 로고
    • Ensembl 2002: Accommodating comparative genomics
    • Clamp, M. et al. Ensembl 2002: accommodating comparative genomics. Nucleic Acids Res. 31, 38-42 (2003).
    • (2003) Nucleic Acids Res. , vol.31 , pp. 38-42
    • Clamp, M.1
  • 97
    • 0036125446 scopus 로고    scopus 로고
    • Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA)
    • Lee, Y. et al. Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA). Genome Res. 12, 493-502 (2002).
    • (2002) Genome Res. , vol.12 , pp. 493-502
    • Lee, Y.1
  • 98
    • 0036737423 scopus 로고    scopus 로고
    • OrthoGUI: Graphical presentation of Orthostrapper results
    • Hollich, V., Storm, C. E. & Sonnhammer, E. L. OrthoGUI: graphical presentation of Orthostrapper results. Bionformatics 18, 1272-1273 (2002).
    • (2002) Bionformatics , vol.18 , pp. 1272-1273
    • Hollich, V.1    Storm, C.E.2    Sonnhammer, E.L.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.