메뉴 건너뛰기




Volumn 25, Issue 12, 2009, Pages

Assessing phylogenetic motif models for predicting transcription factor binding sites

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

EID: 66349125452     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp201     Document Type: Conference Paper
Times cited : (16)

References (33)
  • 1
    • 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. (2002) 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) Proc. Natl Acad. Sci. USA , vol.99 , pp. 757-762
    • Berman, B.P.1
  • 2
    • 1542748076 scopus 로고    scopus 로고
    • Aligning multiple genomic sequences with the threaded blockset aligner
    • Blanchette,M. et al. (2004) Aligning multiple genomic sequences with the threaded blockset aligner. Genome Res., 14, 708-715.
    • (2004) Genome Res , vol.14 , pp. 708-715
    • Blanchette, M.1
  • 3
    • 0242418246 scopus 로고    scopus 로고
    • Phylogenetic shadowing of primate sequences to find functional regions of the human genome
    • Boffelli,D. et al. (2003) Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science, 299, 1391-1394.
    • (2003) Science , vol.299 , pp. 1391-1394
    • Boffelli, D.1
  • 4
    • 34547874585 scopus 로고    scopus 로고
    • Divergence of transcription factor binding sites across related yeast species
    • Borneman,A.R. et al. (2007) Divergence of transcription factor binding sites across related yeast species. Science, 317, 815-819.
    • (2007) Science , vol.317 , pp. 815-819
    • Borneman, A.R.1
  • 5
    • 0037398368 scopus 로고    scopus 로고
    • Lagan and multi-lagan: Efficient tools for large-scale multiple alignment of genomic DNA
    • Brudno,M. et al. (2003) Lagan and multi-lagan: Efficient tools for large-scale multiple alignment of genomic DNA. Genome Res., 13 721-731.
    • (2003) Genome Res , vol.13 , pp. 721-731
    • Brudno, M.1
  • 6
    • 0042121237 scopus 로고    scopus 로고
    • Multiple sequence alignment with the clustal series of programs
    • Chenna,R. et al. (2003) Multiple sequence alignment with the clustal series of programs. Nucleic Acids Res., 31, 3497-3500.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3497-3500
    • Chenna, R.1
  • 7
    • 34249723155 scopus 로고    scopus 로고
    • Frequent gain and loss of functional transcription factor binding sites
    • Doniger,S.W. and Fay,J.C. (2007) Frequent gain and loss of functional transcription factor binding sites. PLoS Comput. Biol., 3, e99.
    • (2007) PLoS Comput. Biol , vol.3
    • Doniger, S.W.1    Fay, J.C.2
  • 8
    • 14644390333 scopus 로고    scopus 로고
    • A model of the statistical power of comparative genome sequence analysis
    • Eddy,S.R. (2005) A model of the statistical power of comparative genome sequence analysis. PLoS Biol., 3, e10.
    • (2005) PLoS Biol , vol.3
    • Eddy, S.R.1
  • 9
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein,J. (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J. Mol. Evol., 17, 368-376.
    • (1981) J. Mol. Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 10
    • 58149354385 scopus 로고    scopus 로고
    • Analysis of combinatorial cis-regulation in synthetic and genomic promoters
    • Gertz,J. (2008) Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature, 457, 215-218.
    • (2008) Nature , vol.457 , pp. 215-218
    • Gertz, J.1
  • 11
    • 33745737494 scopus 로고    scopus 로고
    • Myc-binding-site recognition in the human genome is determined by chromatin context
    • 764-U225
    • Guccione,E. (2006) Myc-binding-site recognition in the human genome is determined by chromatin context. Nat. Cell Biol., 8, 764-U225.
    • (2006) Nat. Cell Biol , vol.8
    • Guccione, E.1
  • 12
    • 33746835021 scopus 로고    scopus 로고
    • Computational identification of transcriptional regulatory elements in DNA sequence
    • GuhaThakurta,D. (2006) Computational identification of transcriptional regulatory elements in DNA sequence. Nucleic Acids Res., 34, 3585-3598.
    • (2006) Nucleic Acids Res , vol.34 , pp. 3585-3598
    • GuhaThakurta, D.1
  • 13
    • 0026738749 scopus 로고
    • Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes
    • Gumucio,D.L. et al. (1992) Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes. Mol. Cell Biol., 12, 4919-4929.
    • (1992) Mol. Cell Biol , vol.12 , pp. 4919-4929
    • Gumucio, D.L.1
  • 14
    • 0031875569 scopus 로고    scopus 로고
    • Evolutionary distances for protein-coding sequences: Modeling site-specific residue frequencies
    • Halpern,A.L. and Bruno,W.J. (1998) Evolutionary distances for protein-coding sequences: Modeling site-specific residue frequencies. Mol. Biol. Evol., 15, 910-917.
    • (1998) Mol. Biol. Evol , vol.15 , pp. 910-917
    • Halpern, A.L.1    Bruno, W.J.2
  • 15
    • 0022376704 scopus 로고
    • Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
    • Hasegawa,M. et al. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol., 22, 160-174.
    • (1985) J. Mol. Evol , vol.22 , pp. 160-174
    • Hasegawa, M.1
  • 17
    • 0037100671 scopus 로고    scopus 로고
    • Mafft: A novel method for rapid multiple sequence alignment based on fast fourier transform
    • Katoh,K. et al. (2002) Mafft: A novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res., 30, 3059-3066.
    • (2002) Nucleic Acids Res , vol.30 , pp. 3059-3066
    • Katoh, K.1
  • 18
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • Kellis,M. et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, 423, 241-254.
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1
  • 19
    • 38849171836 scopus 로고    scopus 로고
    • Reliable prediction of regulator targets using 12 Drosophila genomes
    • Kheradpour,P. et al. (2007) Reliable prediction of regulator targets using 12 Drosophila genomes. Genome Res., 17, 1919-1931.
    • (2007) Genome Res , vol.17 , pp. 1919-1931
    • Kheradpour, P.1
  • 20
    • 33847076849 scopus 로고    scopus 로고
    • Chromatin modifications and their function
    • Kouzarides,T. (2007) Chromatin modifications and their function. Cell 128, 693-705.
    • (2007) Cell , vol.128 , pp. 693-705
    • Kouzarides, T.1
  • 21
    • 0037819447 scopus 로고    scopus 로고
    • Transcription regulation and animal diversity
    • Levine,M. and Tjian,R. (2003) Transcription regulation and animal diversity. Nature, 424, 147-151.
    • (2003) Nature , vol.424 , pp. 147-151
    • Levine, M.1    Tjian, R.2
  • 22
    • 33749381311 scopus 로고    scopus 로고
    • Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection
    • Liu,X. (2006) Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Res., 16, 1517-1528.
    • (2006) Genome Res , vol.16 , pp. 1517-1528
    • Liu, X.1
  • 23
    • 22144491990 scopus 로고    scopus 로고
    • MONKEY: Identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model
    • Moses,A.M. et al. (2004) MONKEY: Identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol., 5, R98.
    • (2004) Genome Biol , vol.5
    • Moses, A.M.1
  • 24
    • 33750442876 scopus 로고    scopus 로고
    • Large-scale turnover of functional transcription factor binding sites in drosophila
    • Moses,A.M. et al. (2006) Large-scale turnover of functional transcription factor binding sites in drosophila. PLoS Comput. Biol. 2, e130.
    • (2006) PLoS Comput. Biol , vol.2
    • Moses, A.M.1
  • 25
    • 36949023082 scopus 로고    scopus 로고
    • A nucleosome-guided map of transcription factor binding sites in yeast
    • Narlikar,L. et al. (2007) A nucleosome-guided map of transcription factor binding sites in yeast. PLos Comput. Biol., 3, e215.
    • (2007) PLos Comput. Biol , vol.3
    • Narlikar, L.1
  • 26
    • 0025265665 scopus 로고
    • Searching for patterns in protein and nucleic acid sequences
    • Staden,R. (1990) Searching for patterns in protein and nucleic acid sequences. Methods Enzymol., 183, 193-211.
    • (1990) Methods Enzymol , vol.183 , pp. 193-211
    • Staden, R.1
  • 28
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: Representation and discovery
    • Stormo,G.D. (2000) DNA binding sites: Representation and discovery. Bioinformatics, 16, 16-23.
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 29
    • 0023890867 scopus 로고
    • Measuring the accuracy of diagnostic systems
    • Swets,J.A. (1988) Measuring the accuracy of diagnostic systems. Science, 240, 1285-1293.
    • (1988) Science , vol.240 , pp. 1285-1293
    • Swets, J.A.1
  • 30
    • 40149098862 scopus 로고    scopus 로고
    • The evolution of combinatorial gene regulation in fungi
    • Tuch,B.B. et al. (2008) The evolution of combinatorial gene regulation in fungi. PLoS Biol., 6, e38.
    • (2008) PLoS Biol , vol.6
    • Tuch, B.B.1
  • 31
    • 1842584947 scopus 로고    scopus 로고
    • Applied bioinformatics for the identification of regulatory elements
    • Wasserman,W.W. and Sandelin,A. (2004) Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet., 5, 276-287.
    • (2004) Nat. Rev. Genet , vol.5 , pp. 276-287
    • Wasserman, W.W.1    Sandelin, A.2
  • 32
    • 58549106607 scopus 로고    scopus 로고
    • High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites
    • Whitington,T. et al. (2008) High-throughput chromatin information enables accurate tissue-specific prediction of transcription factor binding sites. Nucleic Acids Res., 37, 14-25.
    • (2008) Nucleic Acids Res , vol.37 , pp. 14-25
    • Whitington, T.1
  • 33
    • 0032861774 scopus 로고    scopus 로고
    • SCPD: A promoter database of the yeast Saccharomyces cerevisiae
    • Zhu,J. and Zhang,M.Q. (1999) SCPD: A promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15, 607-611.
    • (1999) Bioinformatics , vol.15 , pp. 607-611
    • Zhu, J.1    Zhang, M.Q.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.