메뉴 건너뛰기




Volumn 19, Issue 1, 2004, Pages 188-204

Computational discovery of gene regulatory binding motifs: A Bayesian perspective

Author keywords

Bayesian models; Gene regulation; Markov chain Monte Carlo; Motif discovery; Scoring functions, optimization

Indexed keywords


EID: 0346490298     PISSN: 08834237     EISSN: None     Source Type: Journal    
DOI: 10.1214/088342304000000107     Document Type: Review
Times cited : (71)

References (45)
  • 2
    • 0037109192 scopus 로고    scopus 로고
    • Additivity in protein-DNA interactions: How good an approximation is it?
    • BENOS, P. V., BULYK, M. L. and STORMO, G. D. (2002). Additivity in protein-DNA interactions: How good an approximation is it? Nucleic Acids Res. 30 4442-4451.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 4442-4451
    • Benos, P.V.1    Bulyk, M.L.2    Stormo, G.D.3
  • 3
    • 0036977044 scopus 로고    scopus 로고
    • Probabilistic code for DNA recognition by proteins of the EGR family
    • BENOS, P. V., LAPEDES, A. S. and STORMO, G. D. (2002). Probabilistic code for DNA recognition by proteins of the EGR family. J. Molecular Biol. 323 701-727.
    • (2002) J. Molecular Biol. , vol.323 , pp. 701-727
    • Benos, P.V.1    Lapedes, A.S.2    Stormo, G.D.3
  • 5
    • 0032413411 scopus 로고    scopus 로고
    • Predicting gene regulatory elements in silico on a genomic scale
    • BRAZMA, A., JONASSEN, I., VILO, J. and UKKONEN, E. (1998). Predicting gene regulatory elements in silico on a genomic scale. Genome Res. 8 1202-1215.
    • (1998) Genome Res. , vol.8 , pp. 1202-1215
    • Brazma, A.1    Jonassen, I.2    Vilo, J.3    Ukkonen, E.4
  • 6
    • 1242316281 scopus 로고    scopus 로고
    • ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments
    • BUCK, M. J. and LIEB, J. D. (2004). ChIP-chip: Considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83 349-360.
    • (2004) Genomics , vol.83 , pp. 349-360
    • Buck, M.J.1    Lieb, J.D.2
  • 7
    • 0034730161 scopus 로고    scopus 로고
    • Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis
    • BUSSEMAKER, H. J., LI, H. and SIGGIA, E. D. (2000). Building a dictionary for genomes: Identification of presumptive regulatory sites by statistical analysis. Proc. Natl. Acad. Sci. U.S.A. 97 10,096-10,100.
    • (2000) Proc. Natl. Acad. Sci. U.S.A. , vol.97
    • Bussemaker, H.J.1    Li, H.2    Siggia, E.D.3
  • 8
    • 0026602181 scopus 로고
    • Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments
    • CARDON, L. R. and STORMO, G. D. (1992). Expectation maximization algorithm for identifying protein-binding sites with variable lengths from unaligned DNA fragments. J. Molecular Biol. 223 159-170.
    • (1992) J. Molecular Biol. , vol.223 , pp. 159-170
    • Cardon, L.R.1    Stormo, G.D.2
  • 9
    • 0037453009 scopus 로고    scopus 로고
    • Integrating regulatory motif discovery and genome-wide expression analysis
    • CONLON, E. M., LIU, X. S., LIEB, J. D. and LIU, J. S. (2003). Integrating regulatory motif discovery and genome-wide expression analysis. Proc. Natl. Acad. Sci. U.S.A. 100 3339-3344.
    • (2003) Proc. Natl. Acad. Sci. U.S.A. , vol.100 , pp. 3339-3344
    • Conlon, E.M.1    Liu, X.S.2    Lieb, J.D.3    Liu, J.S.4
  • 11
    • 0042121118 scopus 로고    scopus 로고
    • Cluster-buster: Finding dense clusters of motifs in DNA sequences
    • FRITH, M. C., LI, M. C. and WENG, Z. (2003). Cluster-Buster: Finding dense clusters of motifs in DNA sequences. Nucleic Acids Res. 31 3666-3668.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3666-3668
    • Frith, M.C.1    Li, M.C.2    Weng, Z.3
  • 12
    • 0022358896 scopus 로고
    • Rigorous pattern-recognition methods for DNA sequences
    • Analysis of promoter sequences from
    • GALAS, D. J., EGGERT, M. and WATERMAN, M. S. (1985). Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli. J. Molecular Biol. 186 117-128.
    • (1985) Escherichia Coli. J. Molecular Biol. , vol.186 , pp. 117-128
    • Galas, D.J.1    Eggert, M.2    Waterman, M.S.3
  • 14
    • 0029962489 scopus 로고    scopus 로고
    • ParaMEME: A parallel implementation and a web interface for a DNA and protein motif discovery tool
    • GRUNDY, W. N., BAILEY, T. L. and ELKAN, C. P. (1996). ParaMEME: A parallel implementation and a web interface for a DNA and protein motif discovery tool. Computer Applications in the Biosciences 12 303-310.
    • (1996) Computer Applications in the Biosciences , vol.12 , pp. 303-310
    • Grundy, W.N.1    Bailey, T.L.2    Elkan, C.P.3
  • 15
    • 0037361669 scopus 로고    scopus 로고
    • Discovery of conserved sequence patterns using a stochastic dictionary model
    • GUPTA, M. and LIU, J. S. (2003). Discovery of conserved sequence patterns using a stochastic dictionary model. J. Amer. Statist. Assoc. 98 55-66.
    • (2003) J. Amer. Statist. Assoc. , vol.98 , pp. 55-66
    • Gupta, M.1    Liu, J.S.2
  • 17
    • 0032826179 scopus 로고    scopus 로고
    • Identifying DNA and protein patterns with statistically significant alignments of multiple sequences
    • HERTZ, G. Z. and STORMO, G. D. (1999). Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics 15 563-577.
    • (1999) Bioinformatics , vol.15 , pp. 563-577
    • Hertz, G.Z.1    Stormo, G.D.2
  • 18
    • 2042437650 scopus 로고    scopus 로고
    • Initial sequencing and analysis of the human genome
    • INTERNATIONAL HUMAN GENOME SEQUENCING CONSORTIUM (2001). Initial sequencing and analysis of the human genome. Nature 409 860-921.
    • (2001) Nature , vol.409 , pp. 860-921
  • 19
    • 85045799952 scopus 로고
    • Nomenclature for incompletely specified bases in nucleic acid sequences. Recommendations 1984
    • IUPAC, Nomenclature Committee of the International Union of Biochemistry (NC-IUB) (1986). Nomenclature for incompletely specified bases in nucleic acid sequences. Recommendations 1984. Proc. Natl. Acad. Sci. U.S.A. 83 4-8.
    • (1986) Proc. Natl. Acad. Sci. U.S.A. , vol.83 , pp. 4-8
  • 21
    • 0036772332 scopus 로고    scopus 로고
    • Finding motifs in the twilight zone
    • KEICH, U. and PEVZNER, P. A. (2002). Finding motifs in the twilight zone. Bioinformatics 18 1374-1381.
    • (2002) Bioinformatics , vol.18 , pp. 1374-1381
    • Keich, U.1    Pevzner, P.A.2
  • 22
    • 26444479778 scopus 로고
    • Optimization by simulated annealing
    • KIRKPATRICK, S., GELATT, C. D. and VECCHI, M. P. (1983). Optimization by simulated annealing. Science 220 671-680.
    • (1983) Science , vol.220 , pp. 671-680
    • Kirkpatrick, S.1    Gelatt, C.D.2    Vecchi, M.P.3
  • 23
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
    • LAWRENCE, C. E., ALTSCHUL, S. F., BOGUSKI, M. S., LIU, J. S., NEUWALD, A. F. and WOOTTON, J. C. (1993). Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science 262 208-214.
    • (1993) Science , vol.262 , pp. 208-214
    • Lawrence, C.E.1    Altschul, S.F.2    Boguski, M.S.3    Liu, J.S.4    Neuwald, A.F.5    Wootton, J.C.6
  • 24
    • 0025320805 scopus 로고
    • An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences
    • LAWRENCE, C. E. and REILLY, A. A. (1990). An expectation maximization (EM) algorithm for the identification and characterization of common sites in unaligned biopolymer sequences. Proteins 7 41-51.
    • (1990) Proteins , vol.7 , pp. 41-51
    • Lawrence, C.E.1    Reilly, A.A.2
  • 25
    • 79951870792 scopus 로고
    • The collapsed Gibbs sampler in Bayesian computations with applications to a gene regulation problem
    • LIU, J. S. (1994). The collapsed Gibbs sampler in Bayesian computations with applications to a gene regulation problem. J. Amer. Statist. Assoc. 89 958-966.
    • (1994) J. Amer. Statist. Assoc. , vol.89 , pp. 958-966
    • Liu, J.S.1
  • 26
    • 84950424966 scopus 로고
    • Bayesian models for multiple local sequence alignment and Gibbs sampling strategies
    • LIU, J. S., NEUWALD, A. F. and LAWRENCE, C. E. (1995). Bayesian models for multiple local sequence alignment and Gibbs sampling strategies. J. Amer. Statist. Assoc. 90 1156-1170.
    • (1995) J. Amer. Statist. Assoc. , vol.90 , pp. 1156-1170
    • Liu, J.S.1    Neuwald, A.F.2    Lawrence, C.E.3
  • 27
  • 28
    • 0035228215 scopus 로고    scopus 로고
    • BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
    • LIU, X. S., BRUTLAG, D. L. and LIU, J. S. (2001). BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pacific Symposium on Biocomputing 6 127-138.
    • (2001) Pacific Symposium on Biocomputing , vol.6 , pp. 127-138
    • Liu, X.S.1    Brutlag, D.L.2    Liu, J.S.3
  • 29
    • 0036324753 scopus 로고    scopus 로고
    • An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarray experiments
    • LIU, X. S., BRUTLAG, D. L. and LIU, J. S. (2002). An algorithm for finding protein-DNA binding sites with applications to chromatin immunoprecipitation microarray experiments. Nature Biotechnology 20 835-839.
    • (2002) Nature Biotechnology , vol.20 , pp. 835-839
    • Liu, X.S.1    Brutlag, D.L.2    Liu, J.S.3
  • 30
    • 0008533463 scopus 로고
    • Regulation of transcription initiation
    • J. Darnell, H. Lodish and D. Baltimore, eds. Scientific American Books, New York
    • LODISH, H., BALTIMORE, D., BERK, A., ZIPURSKY, S. L., MATSUDAIRA, P. and DARNELL, J. (1995). Regulation of transcription initiation. In Molecular Cell Biology, 3rd ed. (J. Darnell, H. Lodish and D. Baltimore, eds.) 405-481. Scientific American Books, New York.
    • (1995) Molecular Cell Biology, 3rd Ed. , pp. 405-481
    • Lodish, H.1    Baltimore, D.2    Berk, A.3    Zipursky, S.L.4    Matsudaira, P.5    Darnell, J.6
  • 32
    • 0029144601 scopus 로고
    • Gibbs motif sampling: Detection of bacterial outer membrane protein repeats
    • NEUWALD, A. F., LIU, J. S. and LAWRENCE, C. E. (1995). Gibbs motif sampling: Detection of bacterial outer membrane protein repeats. Protein Science 4 1618-1632.
    • (1995) Protein Science , vol.4 , pp. 1618-1632
    • Neuwald, A.F.1    Liu, J.S.2    Lawrence, C.E.3
  • 33
    • 0019887806 scopus 로고
    • Characteristics of tight-binding repressors of the lac operon
    • PFAHL, M. (1981). Characteristics of tight-binding repressors of the lac operon. J. Molecular Biol. 147 1-10.
    • (1981) J. Molecular Biol. , vol.147 , pp. 1-10
    • Pfahl, M.1
  • 34
    • 0031787969 scopus 로고    scopus 로고
    • Finding DNA regulatory motifs within unaligned non-coding sequences clustered by whole-genome mRNA quantitation
    • ROTH, F. P., HUGHES, J. D., ESTEP, P. W. and CHURCH, G. M. (1998). Finding DNA regulatory motifs within unaligned non-coding sequences clustered by whole-genome mRNA quantitation. Nature Biotechnology 16 939-945.
    • (1998) Nature Biotechnology , vol.16 , pp. 939-945
    • Roth, F.P.1    Hughes, J.D.2    Estep, P.W.3    Church, G.M.4
  • 35
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • SCHENA, M., SHALON, D., DAVIS, R. W. and BROWN, P. O. (1995). Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270 467-470.
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 38
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: Representation and discovery
    • STORMO, G. D. (2000). DNA binding sites: Representation and discovery. Bioinfomatics 16 16-23.
    • (2000) Bioinfomatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 39
    • 0000133199 scopus 로고
    • Identifying protein-binding sites from unaligned DNA fragments
    • STORMO, G. D. and HARTZELL, G. W. (1989). Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl. Acad. Sci. U.S.A. 86 1183-1187.
    • (1989) Proc. Natl. Acad. Sci. U.S.A. , vol.86 , pp. 1183-1187
    • Stormo, G.D.1    Hartzell, G.W.2
  • 40
    • 84950758368 scopus 로고
    • The calculation of posterior distributions by data augmentation
    • TANNER, M. A. and WONG, W. H. (1987). The calculation of posterior distributions by data augmentation (with discussion). J. Amer. Statist. Assoc. 82 528-550.
    • (1987) J. Amer. Statist. Assoc. , vol.82 , pp. 528-550
    • Tanner, M.A.1    Wong, W.H.2
  • 41
    • 0032483307 scopus 로고    scopus 로고
    • Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies
    • VAN HELDEN, J., ANDRE, B. and COLLADO-VIDES, J. (1998). Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Molecular Biol. 281 827-842.
    • (1998) J. Molecular Biol. , vol.281 , pp. 827-842
    • Van Helden, J.1    Andre, B.2    Collado-Vides, J.3
  • 42
    • 0034656326 scopus 로고    scopus 로고
    • Discovering regulatory elements in non-coding sequences by analysis of spaced dyads
    • VAN HELDEN, J., RIOS, A. F. and COLLADO-VIDES, J. (2000). Discovering regulatory elements in non-coding sequences by analysis of spaced dyads. Nucleic Acids Res. 28 1808-1818.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1808-1818
    • Van Helden, J.1    Rios, A.F.2    Collado-Vides, J.3
  • 44
    • 0032776529 scopus 로고    scopus 로고
    • Models for prediction and recognition of eukaryotic promoters
    • WERNER, T. (1999). Models for prediction and recognition of eukaryotic promoters. Mammalian Genome 10 168-175.
    • (1999) Mammalian Genome , vol.10 , pp. 168-175
    • Werner, T.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.