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Volumn 6, Issue 13, 2005, Pages

A novel approach to identifying regulatory motifs in distantly related genomes

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BINDING SITE; CONSENSUS SEQUENCE; CONTROLLED STUDY; DATA BASE; GENE CONTROL; GENE SEQUENCE; GENOME ANALYSIS; GENOME SIZE; HUMAN; METHODOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; AMINO ACID SEQUENCE; ANIMAL; BASE PAIRING; BIOLOGY; CHEMISTRY; GENETIC DATABASE; GENETICS; GENOME; MOLECULAR GENETICS; REGULATORY SEQUENCE;

EID: 33745106601     PISSN: 1474760X     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2005-6-13-r113     Document Type: Article
Times cited : (11)

References (76)
  • 1
    • 0023821768 scopus 로고
    • Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints
    • Tagle DA, Koop BF, Goodman M, Slightom JL, Hess DL, Jones RT: Embryonic epsilon and gamma globin genes of a prosimian primate (Galago crassicaudatus). Nucleotide and amino acid sequences, developmental regulation and phylogenetic footprints. J Mol Biol 1988, 203:439-455.
    • (1988) J Mol Biol , vol.203 , pp. 439-455
    • Tagle, D.A.1    Koop, B.F.2    Goodman, M.3    Slightom, J.L.4    Hess, D.L.5    Jones, R.T.6
  • 2
    • 0033976523 scopus 로고    scopus 로고
    • Discovery and modeling of transcriptional regulatory regions
    • Fickett JW, Wasserman WW: Discovery and modeling of transcriptional regulatory regions. Curr Opin Biotechnol 2000, 11:19-24.
    • (2000) Curr Opin Biotechnol , vol.11 , pp. 19-24
    • Fickett, J.W.1    Wasserman, W.W.2
  • 3
    • 0034783060 scopus 로고    scopus 로고
    • Enrichment of regulatory signals in conserved non-coding genomic sequence
    • Levy S, Hannenhalli S, Workman C: Enrichment of regulatory signals in conserved non-coding genomic sequence. Bioinformatics 2001, 17:871-877.
    • (2001) Bioinformatics , vol.17 , pp. 871-877
    • Levy, S.1    Hannenhalli, S.2    Workman, C.3
  • 5
    • 1242296821 scopus 로고    scopus 로고
    • Analysis of multiple genomic sequence alignments: A web resource, online tools, and lessons learned from analysis of mammalian SCL loci
    • Chapman MA, Donaldson IJ, Gilbert J, Grafham D, Rogers J, Green AR, Gottgens B: Analysis of multiple genomic sequence alignments: a web resource, online tools, and lessons learned from analysis of mammalian SCL loci. Genome Res 2004. 14:313-318.
    • (2004) Genome Res , vol.14 , pp. 313-318
    • Chapman, M.A.1    Donaldson, I.J.2    Gilbert, J.3    Grafham, D.4    Rogers, J.5    Green, A.R.6    Gottgens, B.7
  • 6
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson JD, Higgins DG, Gibson TJ: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 7
    • 0031854952 scopus 로고    scopus 로고
    • DIALIGN: Finding local similarities by multiple sequence alignment
    • Morgenstern B, Frech K, Dress A, Werner T: DIALIGN: finding local similarities by multiple sequence alignment. Bioinformatics 1998, 14:290-294.
    • (1998) Bioinformatics , vol.14 , pp. 290-294
    • Morgenstern, B.1    Frech, K.2    Dress, A.3    Werner, T.4
  • 8
    • 0032945593 scopus 로고    scopus 로고
    • DIALIGN 2: Improvement of the segment-to-segment approach to multiple sequence alignment
    • Morgenstern B: DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment. Bioinformatics 1999, 15:211-218.
    • (1999) Bioinformatics , vol.15 , pp. 211-218
    • Morgenstern, B.1
  • 9
    • 0042121222 scopus 로고    scopus 로고
    • MAVID multiple alignment server
    • Bray N, Pachter L: MAVID multiple alignment server. Nucleic Acids Res 2003, 31:3525-3526.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3525-3526
    • Bray, N.1    Pachter, L.2
  • 10
    • 1842667852 scopus 로고    scopus 로고
    • MAVID: Constrained ancestral alignment of multiple sequences
    • Bray N, Pachter L: MAVID: constrained ancestral alignment of multiple sequences. Genome Res 2004, 14:693-699.
    • (2004) Genome Res , vol.14 , pp. 693-699
    • Bray, N.1    Pachter, L.2
  • 12
    • 1242272082 scopus 로고    scopus 로고
    • Identification of a gadd45beta 3′ enhancer that mediates SMAD3- and SMAD4-dependent transcriptional induction by transforming growth factor beta
    • Major MB, Jones DA: Identification of a gadd45beta 3′ enhancer that mediates SMAD3- and SMAD4-dependent transcriptional induction by transforming growth factor beta. J Biol Chem 2004, 279:5278-5287.
    • (2004) J Biol Chem , vol.279 , pp. 5278-5287
    • Major, M.B.1    Jones, D.A.2
  • 13
    • 0032562789 scopus 로고    scopus 로고
    • Identification of regulatory regions which confer muscle-specific gene expression
    • Wasserman WW, Fickett JW: Identification of regulatory regions which confer muscle-specific gene expression. J Mol Biol 1998, 278:167-181.
    • (1998) J Mol Biol , vol.278 , pp. 167-181
    • Wasserman, W.W.1    Fickett, J.W.2
  • 16
    • 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 2001, 78:73-82.
    • (2001) Genomics , vol.78 , pp. 73-82
    • Bagheri-Fam, S.1    Ferraz, C.2    Demaille, J.3    Scherer, G.4    Pfeifer, D.5
  • 17
    • 0035821711 scopus 로고    scopus 로고
    • Comparative analysis of the ETV6 gene in vertebrate genomes from pufferfish to human
    • Montpetit A, Sinnett D: Comparative analysis of the ETV6 gene in vertebrate genomes from pufferfish to human. Oncogene 2001, 20:3437-3442.
    • (2001) Oncogene , vol.20 , pp. 3437-3442
    • Montpetit, A.1    Sinnett, D.2
  • 18
  • 19
    • 0038817801 scopus 로고    scopus 로고
    • Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters
    • Santini S, Boore JL, Meyer A: Evolutionary conservation of regulatory elements in vertebrate Hox gene clusters. Genome Res 2003, 13:1111-1122.
    • (2003) Genome Res , vol.13 , pp. 1111-1122
    • Santini, S.1    Boore, J.L.2    Meyer, A.3
  • 23
    • 0027507739 scopus 로고
    • Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome
    • Brenner S, Elgar G, Sandford R, Macrae A, Venkatesh B, Aparicio S: Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature 1993, 366:265-268.
    • (1993) Nature , vol.366 , pp. 265-268
    • Brenner, S.1    Elgar, G.2    Sandford, R.3    Macrae, A.4    Venkatesh, B.5    Aparicio, S.6
  • 24
    • 0034733948 scopus 로고    scopus 로고
    • Fugu: A compact vertebrate reference genome
    • Venkatesh B, Gilligan P, Brenner S: Fugu: a compact vertebrate reference genome. FEBS Lett 2000, 476:3-7.
    • (2000) FEBS Lett , vol.476 , pp. 3-7
    • Venkatesh, B.1    Gilligan, P.2    Brenner, S.3
  • 25
    • 22344437987 scopus 로고    scopus 로고
    • Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach
    • Elemento O, Tavazoie S: Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol 2005, 6:1-R18.
    • (2005) Genome Biol , vol.6
    • Elemento, O.1    Tavazoie, S.2
  • 26
    • 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 Res 2002, 12:739-748.
    • (2002) Genome Res , vol.12 , pp. 739-748
    • Blanchette, M.1    Tompa, M.2
  • 27
    • 0041589546 scopus 로고    scopus 로고
    • FootPrinter: A program designed for phylogenetic footprinting
    • Blanchette M, Tompa M: FootPrinter: A program designed for phylogenetic footprinting. Nucleic Acids Res 2003, 31:3840-3842.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3840-3842
    • Blanchette, M.1    Tompa, M.2
  • 28
    • 0029197507 scopus 로고
    • The value of prior knowledge in discovering motifs with MEME
    • Bailey TL, Elkan C: The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 1995, 3:21-29.
    • (1995) Proc Int Conf Intell Syst Mol Biol , vol.3 , pp. 21-29
    • Bailey, T.L.1    Elkan, C.2
  • 29
    • 0025372992 scopus 로고
    • Identification of consensus patterns in unaligned DNA sequences known to be functionally related
    • Hertz GZ, Hartzell GW III, Stormo GD: Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput Appl Biosci 1990, 6:81-92.
    • (1990) Comput Appl Biosci , vol.6 , pp. 81-92
    • Hertz, G.Z.1    Hartzell III, G.W.2    Stormo, G.D.3
  • 30
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • Hertz GZ, Stormo GD: Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 1999, 15:563-577.
    • (1999) Bioinformatics , vol.15 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 34
    • 0034628901 scopus 로고    scopus 로고
    • Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
    • Hughes JD, Estep PW, Tavazoie S, Church GM: Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 2000, 296:1205-1214.
    • (2000) J Mol Biol , vol.296 , pp. 1205-1214
    • Hughes, J.D.1    Estep, P.W.2    Tavazoie, S.3    Church, G.M.4
  • 35
    • 0033655171 scopus 로고    scopus 로고
    • ANN-Spec: A method for discovering transcription factor binding sites with improved specificity
    • Workman CT, Stormo GD: ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. Pac Symp Biocomput 2000:467-478.
    • (2000) Pac Symp Biocomput , pp. 467-478
    • Workman, C.T.1    Stormo, G.D.2
  • 36
    • 0035228215 scopus 로고    scopus 로고
    • BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
    • Liu X, Brutlag DL, Liu JS: BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac Symp Biocomput 2001:127-138.
    • (2001) Pac Symp Biocomput , pp. 127-138
    • Liu, X.1    Brutlag, D.L.2    Liu, J.S.3
  • 37
    • 0036137323 scopus 로고    scopus 로고
    • A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling
    • Thijs G, Lescot M, Marchal K, Rombauts S, De Moor B, Rouze P, Moreau Y: A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics 2001, 17:1113-1122.
    • (2001) Bioinformatics , vol.17 , pp. 1113-1122
    • Thijs, G.1    Lescot, M.2    Marchal, K.3    Rombauts, S.4    De Moor, B.5    Rouze, P.6    Moreau, Y.7
  • 39
    • 0036108622 scopus 로고    scopus 로고
    • A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes
    • Thijs G, Marchal K, Lescot M, Rombauts S, De Moor B, Rouze P, Moreau Y: A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J Comput Biol 2002, 9:447-464.
    • (2002) J Comput Biol , vol.9 , pp. 447-464
    • Thijs, G.1    Marchal, K.2    Lescot, M.3    Rombauts, S.4    De Moor, B.5    Rouze, P.6    Moreau, Y.7
  • 41
    • 0038354776 scopus 로고    scopus 로고
    • Insights from human/mouse genome comparisons
    • Pennacchio LA: Insights from human/mouse genome comparisons. Mamm Genome 2003, 14:429-436.
    • (2003) Mamm Genome , vol.14 , pp. 429-436
    • Pennacchio, L.A.1
  • 43
    • 0038631908 scopus 로고    scopus 로고
    • In silico identification of metazoan transcriptional regulatory regions
    • Wasserman WW, Krivan W: In silico identification of metazoan transcriptional regulatory regions. Naturwissenschaften 2003, 90:156-166.
    • (2003) Naturwissenschaften , vol.90 , pp. 156-166
    • Wasserman, W.W.1    Krivan, W.2
  • 44
    • 33745088574 scopus 로고    scopus 로고
    • Supplementary Website
    • Supplementary Website [http://homes.esat.kuleuven.be/~kmarchal/ Supplementary_Information_VanHel_2005/SuppWebsite.html]
  • 46
    • 0037108396 scopus 로고    scopus 로고
    • Evolutionary divergence of vertebrate Hoxb2 expression patterns and transcriptional regulatory loci
    • Scemama JL, Hunter M, McCallum J, Prince V, Stellwag E: Evolutionary divergence of vertebrate Hoxb2 expression patterns and transcriptional regulatory loci. J Exp Zool 2002, 294:285-299.
    • (2002) J Exp Zool , vol.294 , pp. 285-299
    • Scemama, J.L.1    Hunter, M.2    McCallum, J.3    Prince, V.4    Stellwag, E.5
  • 47
    • 0032895297 scopus 로고    scopus 로고
    • Distinct cis-essential modules direct the time-space pattern of the Pax6 gene activity
    • Kammandel B, Chowdhury K, Stoykova A, Aparicio S, Brenner S, Gruss P: Distinct cis-essential modules direct the time-space pattern of the Pax6 gene activity. Dev Biol 1999, 205:79-97.
    • (1999) Dev Biol , vol.205 , pp. 79-97
    • Kammandel, B.1    Chowdhury, K.2    Stoykova, A.3    Aparicio, S.4    Brenner, S.5    Gruss, P.6
  • 50
    • 33745065084 scopus 로고    scopus 로고
    • UCSC Genome Browser
    • UCSC Genome Browser [http://genome.ucsc.edu/]
  • 53
    • 33745103340 scopus 로고    scopus 로고
    • UCR Browser
    • UCR Browser [http://mordor.cgb.ki.se/UCRbrowse/]
  • 54
    • 0036226603 scopus 로고    scopus 로고
    • BLAT - The BLAST-like alignment tool
    • Kent WJ: BLAT - the BLAST-like alignment tool. Genome Res 2002, 12:656-664.
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 56
    • 10744222156 scopus 로고    scopus 로고
    • Identification and characterization of multi-species conserved sequences
    • Margulies EH, Blanchette M, Haussler D, Green ED: Identification and characterization of multi-species conserved sequences. Genome Res 2003, 13:2507-2518.
    • (2003) Genome Res , vol.13 , pp. 2507-2518
    • Margulies, E.H.1    Blanchette, M.2    Haussler, D.3    Green, E.D.4
  • 57
    • 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. Nat Rev Genet 2003, 4:251-262.
    • (2003) Nat Rev Genet , vol.4 , pp. 251-262
    • Ureta-Vidal, A.1    Ettwiller, L.2    Birney, E.3
  • 58
    • 3042740671 scopus 로고    scopus 로고
    • Comparative genomics at the vertebrate extremes
    • Boffelli D, Nobrega MA, Rubin EM: Comparative genomics at the vertebrate extremes. Nat Rev Genet 2004, 5:456-465.
    • (2004) Nat Rev Genet , vol.5 , pp. 456-465
    • Boffelli, D.1    Nobrega, M.A.2    Rubin, E.M.3
  • 59
    • 7444260846 scopus 로고    scopus 로고
    • The ENCODE (ENCyclopedia Of DNA Elements) Project
    • Encode Project Consortium
    • Encode Project Consortium: The ENCODE (ENCyclopedia Of DNA Elements) Project. Science 2004, 306:636-640.
    • (2004) Science , vol.306 , pp. 636-640
  • 61
    • 14944363825 scopus 로고    scopus 로고
    • NestedMICA: Sensitive inference of over-represented motifs in nucleic acid sequence
    • Down TA, Hubbard TJ: NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence. Nucleic Acids Res 2005, 33:1445-1453.
    • (2005) Nucleic Acids Res , vol.33 , pp. 1445-1453
    • Down, T.A.1    Hubbard, T.J.2
  • 62
    • 33745073716 scopus 로고    scopus 로고
    • Ensembl Genome Browser
    • Ensembl Genome Browser [http://www.ensembl.org]
  • 64
    • 0032964297 scopus 로고    scopus 로고
    • BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences
    • Tatusova TA, Madden TL: BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol Lett 1999, 174:247-250.
    • (1999) FEMS Microbiol Lett , vol.174 , pp. 247-250
    • Tatusova, T.A.1    Madden, T.L.2
  • 65
    • 0037270315 scopus 로고    scopus 로고
    • AVID: A global alignment program
    • Bray N, Dubchak I, Pachter L: AVID: A global alignment program. Genome Res 2003, 13:97-102.
    • (2003) Genome Res , vol.13 , pp. 97-102
    • Bray, N.1    Dubchak, I.2    Pachter, L.3
  • 67
    • 0036529479 scopus 로고    scopus 로고
    • An efficient algorithm for large-scale detection of protein families
    • Enright AJ, Van Dongen S, Ouzounis CA: An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 2002, 30:1575-1584.
    • (2002) Nucleic Acids Res , vol.30 , pp. 1575-1584
    • Enright, A.J.1    Van Dongen, S.2    Ouzounis, C.A.3
  • 69
    • 33745091087 scopus 로고    scopus 로고
    • BLAT Search Genome
    • BLAT Search Genome [http://genome.ucsc.edu/cgi-bin/hgBlat]
  • 72
    • 33745058024 scopus 로고    scopus 로고
    • BiolΣCD Software
    • BiolΣCD Software [http://homes.esat.kuleuven.be/~dna/Bioi/ Software.html]
  • 73
    • 13544254744 scopus 로고    scopus 로고
    • Identifying combinatorial regulation of transcription factors and binding motifs
    • Kato M, Hata N, Banerjee N, Futcher B, Zhang MQ: Identifying combinatorial regulation of transcription factors and binding motifs. Genome Biol 2004, 5:R56.1-R56.13.
    • (2004) Genome Biol , vol.5
    • Kato, M.1    Hata, N.2    Banerjee, N.3    Futcher, B.4    Zhang, M.Q.5
  • 74
    • 33745078892 scopus 로고    scopus 로고
    • MAVID Multiple Alignment Server
    • MAVID Multiple Alignment Server [http://baboon.math.berkeley.edu/mavid/]
  • 75
    • 33745093689 scopus 로고    scopus 로고
    • Miller Lab
    • Miller Lab [http://bio.cse.psu.edu/]
  • 76
    • 33745058939 scopus 로고    scopus 로고
    • E Margulies FTP Site [ftp://kronos.nhgri.nih.gov/pub/outgoing/elliott/ tba/]
    • E Margulies FTP Site [ftp://kronos.nhgri.nih.gov/pub/outgoing/elliott/ tba/]


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