메뉴 건너뛰기




Volumn 20, Issue 6, 2004, Pages 909-916

Modeling within-motif dependence for transcription factor binding site predictions

Author keywords

[No Author keywords available]

Indexed keywords

DNA; TRANSCRIPTION FACTOR E2F;

EID: 2342445980     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bth006     Document Type: Article
Times cited : (115)

References (23)
  • 2
    • 0038716277 scopus 로고    scopus 로고
    • Modeling dependence in protein-DNA binding sites
    • RECOMB'03. Berlin, Germany, April 2003
    • Barash, Y., Elidan, G., Friedman ,N. and Kaplan, T. (2003) Modeling dependence in protein-DNA binding sites. RECOMB'03. Berlin, Germany, April 2003.
    • (2003)
    • Barash, Y.1    Elidan, G.2    Friedman, N.3    Kaplan, T.4
  • 3
    • 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. (2002a) 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
  • 4
    • 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. (2002b) Probabilistic code for DNA recognition by proteins of the EGR family. J. Mol. Biol., 323, 701-727.
    • (2002) J. Mol. Biol. , vol.323 , pp. 701-727
    • Benos, P.V.1    Lapedes, A.S.2    Stormo, G.D.3
  • 5
    • 0036493201 scopus 로고    scopus 로고
    • Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors
    • Bulyk, M.L., Johnson, P.L.F. and Church, G.M. (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res., 30, 1255-1261.
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1255-1261
    • Bulyk, M.L.1    Johnson, P.L.F.2    Church, G.M.3
  • 6
    • 0022358896 scopus 로고
    • Rigorous pattern-recognition methods for DNA sequence: Analysis of promoter sequences from Escherichia coli
    • Galas, D.J., Eggert, M. and Waterman, M.S. (1985) Rigorous pattern-recognition methods for DNA sequence: analysis of promoter sequences from Escherichia coli. J. Mol. Biol., 186, 117-128.
    • (1985) J. Mol. Biol. , vol.186 , pp. 117-128
    • Galas, D.J.1    Eggert, M.2    Waterman, M.S.3
  • 7
    • 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. Comput. Appl. Biosci., 12, 303-310.
    • (1996) Comput. Appl. Biosci. , vol.12 , pp. 303-310
    • Grundy, W.N.1    Bailey, T.L.2    Elkan, C.P.3
  • 8
    • 0037361669 scopus 로고    scopus 로고
    • Discovery of sequence patterns using a stochastic dictionary model
    • Gupta, M. and Liu, J.S. (2003) Discovery of sequence patterns using a stochastic dictionary model. J. Amer. Stat. Assoc., 98, 55-66.
    • (2003) J. Amer. Stat. Assoc. , vol.98 , pp. 55-66
    • Gupta, M.1    Liu, J.S.2
  • 9
    • 0034949169 scopus 로고    scopus 로고
    • Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis
    • Ishida, S., Huang, E., Zuzan ,H., Spang, R., Leone, G., West, M. and Nevins, J.R. (2001) Role for E2F in control of both DNA replication and mitotic functions as revealed from DNA microarray analysis. Mol. Cell. Biol., 21, 4684-4699.
    • (2001) Mol. Cell. Biol. , vol.21 , pp. 4684-4699
    • Ishida, S.1    Huang, E.2    Zuzan, H.3    Spang, R.4    Leone, G.5    West, M.6    Nevins, J.R.7
  • 10
    • 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.N. and Wootton, J. (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.N.5    Wootton, J.6
  • 11
    • 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
  • 12
    • 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. JASA, 89, 958-966.
    • (1994) JASA , vol.89 , pp. 958-966
    • Liu, J.S.1
  • 14
    • 0035228215 scopus 로고    scopus 로고
    • BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
    • Liu, X., Brutlag, D.L. and Liu, J.S. (2001) BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput., 6, 127-138.
    • (2001) Pac. Symp. Biocomput. , vol.6 , pp. 127-138
    • Liu, X.1    Brutlag, D.L.2    Liu, J.S.3
  • 15
    • 0036324753 scopus 로고    scopus 로고
    • An algorithm for finding protein-DNA interaction sites with applications to chromatin immunoprecipitation microarray experiments
    • Liu, X., Brutlag, D.L. and Liu, J.S. (2002) An algorithm for finding protein-DNA interaction sites with applications to chromatin immunoprecipitation microarray experiments. Nat. Biotechnol., 20, 835-839.
    • (2002) Nat. Biotechnol. , vol.20 , pp. 835-839
    • Liu, X.1    Brutlag, D.L.2    Liu, J.S.3
  • 16
    • 84950424966 scopus 로고
    • Bayesian models for multiple local sequence alignment and Gibbs sampling strategies
    • Liu, J.S., Neuwald, A.N. and Lawrence, C.E. (1995) Bayesian models for multiple local sequence alignment and Gibbs sampling strategies. JASA, 90, 1156-1170.
    • (1995) JASA , vol.90 , pp. 1156-1170
    • Liu, J.S.1    Neuwald, A.N.2    Lawrence, C.E.3
  • 18
    • 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 Sci., 4, 1618-1632.
    • (1995) Protein Sci. , vol.4 , pp. 1618-1632
    • Neuwald, A.F.1    Liu, J.S.2    Lawrence, C.E.3
  • 19
    • 0037080483 scopus 로고    scopus 로고
    • E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints
    • Ren, B., Cam, H., Takahashi ,Y., Volkert, T., Terragni, J., Young, R.A. and Dynlacht ,B.D. (2002) E2F integrates cell cycle progression with DNA repair, replication, and G(2)/M checkpoints. Genes Dev., 16, 245-256.
    • (2002) Genes Dev. , vol.16 , pp. 245-256
    • Ren, B.1    Cam, H.2    Takahashi, Y.3    Volkert, T.4    Terragni, J.5    Young, R.A.6    Dynlacht, B.D.7
  • 20
    • 0031787969 scopus 로고    scopus 로고
    • Finding DNA regulatory motifs within unaligned non-coding sequences clustered by whole genome mRNA quantization
    • Roth, F.R., Hughes ,J.D., Estep, P.E. and Church ,G.M. (1998) Finding DNA regulatory motifs within unaligned non-coding sequences clustered by whole genome mRNA quantization. Nat. Biotechnol., 16, 939-945.
    • (1998) Nat. Biotechnol. , vol.16 , pp. 939-945
    • Roth, F.R.1    Hughes, J.D.2    Estep, P.E.3    Church, G.M.4
  • 21
    • 0025008168 scopus 로고
    • Sequence logos: A new way to display consensus sequences
    • Schneider, T.D. and Stephens, R.M. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2
  • 22
    • 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., USA, 86, 1183-1187.
    • (1989) Proc. Natl. Acad. Sci. USA , vol.86 , pp. 1183-1187
    • Stormo, G.D.1    Hartzell, G.W.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.