메뉴 건너뛰기




Volumn 32, Issue 13, 2004, Pages 3826-3835

Discovery of sequence motifs related to coexpression of genes using evolutionary computation

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOTIDE; OCTAMER TRANSCRIPTION FACTOR 1; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; TRANSCRIPTION FACTOR;

EID: 3142737815     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkh713     Document Type: Article
Times cited : (87)

References (44)
  • 1
    • 0034714421 scopus 로고    scopus 로고
    • Gene expression data analysis
    • Brazma,A. and Vilo,J. (2000) Gene expression data analysis. FEBS Lett., 480, 17-24.
    • (2000) FEBS Lett. , vol.480 , pp. 17-24
    • Brazma, A.1    Vilo, J.2
  • 2
    • 0033150947 scopus 로고    scopus 로고
    • Regulatory elements and expression profiles
    • Bucher,P. (1999) Regulatory elements and expression profiles. Curr. Opin. Struct. Biol., 9, 400-407.
    • (1999) Curr. Opin. Struct. Biol. , vol.9 , pp. 400-407
    • Bucher, P.1
  • 4
    • 0030669030 scopus 로고    scopus 로고
    • Exploring the metabolic and genetic control of gene expression on a genomic scale
    • DeRisi,J.L., Iyer,V.R. and Brown,P.O. (1997) Exploring the metabolic and genetic control of gene expression on a genomic scale. Science, 278, 680-686.
    • (1997) Science , vol.278 , pp. 680-686
    • DeRisi, J.L.1    Iyer, V.R.2    Brown, P.O.3
  • 6
    • 0032848435 scopus 로고    scopus 로고
    • Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae
    • Wolfsberg,T.G., Gabrielian,A.E., Campbell,M.J., Cho,R.J., Spouge,J.L. and Landsman,D. (1999) Candidate regulatory sequence elements for cell cycle-dependent transcription in Saccharomyces cerevisiae. Genome Res., 9, 775-792.
    • (1999) Genome Res. , vol.9 , pp. 775-792
    • Wolfsberg, T.G.1    Gabrielian, A.E.2    Campbell, M.J.3    Cho, R.J.4    Spouge, J.L.5    Landsman, D.6
  • 7
    • 0032863227 scopus 로고    scopus 로고
    • Large-scale gene expression data analysis: A new challenge to computational biologist
    • Zhang,M.Q. (1999) Large-scale gene expression data analysis: a new challenge to computational biologist. Genome Res., 9, 681-688.
    • (1999) Genome Res. , vol.9 , pp. 681-688
    • Zhang, M.Q.1
  • 8
    • 0035252126 scopus 로고    scopus 로고
    • Identification and analysis of eukaryotic promoters: Recent computational approaches
    • Ohler,U. and Niemann,H. (2001) Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Genet., 17, 56-60.
    • (2001) Trends Genet. , vol.17 , pp. 56-60
    • Ohler, U.1    Niemann, H.2
  • 9
    • 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
  • 10
    • 0031603909 scopus 로고    scopus 로고
    • Calculating the exact probability of language-like patterns in biomolecular sequences
    • Atteson,K. (1998) Calculating the exact probability of language-like patterns in biomolecular sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 17-24.
    • (1998) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.6 , pp. 17-24
    • Atteson, K.1
  • 11
    • 0033289316 scopus 로고    scopus 로고
    • An exact method for finding short motifs in sequences, with application to the ribosome binding site problem
    • Tompa,M. (1999) An exact method for finding short motifs in sequences, with application to the ribosome binding site problem. Proc. Int. Conf. Intell. Syst. Mol. Biol., 7, 262-271.
    • (1999) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.7 , pp. 262-271
    • Tompa, M.1
  • 12
    • 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
  • 13
    • 0034086773 scopus 로고    scopus 로고
    • Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation
    • Jensen,L.J. and Knudsen,S. (2000) Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation. Bioinformatics, 16, 326-333.
    • (2000) Bioinformatics , vol.16 , pp. 326-333
    • Jensen, L.J.1    Knudsen, S.2
  • 14
    • 0034708338 scopus 로고    scopus 로고
    • Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori sigma(80) family of promoter signals
    • Vanet,A., Marsan,L., Labigne,A. and Sagot,M.F. (2000) Inferring regulatory elements from a whole genome. An analysis of Helicobacter pylori sigma(80) family of promoter signals. J. Mol. Biol., 297, 335-353.
    • (2000) J. Mol. Biol. , vol.297 , pp. 335-353
    • Vanet, A.1    Marsan, L.2    Labigne, A.3    Sagot, M.F.4
  • 15
    • 0032483307 scopus 로고    scopus 로고
    • Extracting regulatory sites from upstream region of yeast genes by computational analysis of oligonucleotide frequencies
    • Van Helden,J., André,B. and Collado-Vides,L. (1998) Extracting regulatory sites from upstream region of yeast genes by computational analysis of oligonucleotide frequencies. J. Mol. Biol., 281, 827-842.
    • (1998) J. Mol. Biol. , vol.281 , pp. 827-842
    • Van Helden, J.1    André, B.2    Collado-Vides, L.3
  • 16
    • 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
  • 17
  • 18
    • 0002759539 scopus 로고
    • Unsupervised learning of multiple motifs in biopolymers using expectation maximization
    • Bailey,T. and Elkan,C. (1995) Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning, 21, 51-80.
    • (1995) Machine Learning , vol.21 , pp. 51-80
    • Bailey, T.1    Elkan, C.2
  • 19
    • 0034628901 scopus 로고    scopus 로고
    • Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae
    • Hughes,J.D., Estep,P.W., Tavazoie,S. and Church,G.M. (2000) Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol., 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
  • 20
    • 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
  • 21
    • 0031787969 scopus 로고    scopus 로고
    • Finding DNA regulatory motifs within unaligned noncoding sequence 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 noncoding sequence clustered by whole genome mRNA quantitation. Nat. Biotechol., 16, 939-945.
    • (1998) Nat. Biotechol. , vol.16 , pp. 939-945
    • Roth, F.P.1    Hughes, J.D.2    Estep, P.W.3    Church, G.M.4
  • 22
    • 0033655171 scopus 로고    scopus 로고
    • ANN-SPEC: A method for discoverying transcription binding sites with improved specificity
    • Workman,C.T. and Stormo,G.D. (2000) ANN-SPEC: a method for discoverying transcription binding sites with improved specificity. Pac. Symp. Biocomput., 5, 467-478.
    • (2000) Pac. Symp. Biocomput. , vol.5 , pp. 467-478
    • Workman, C.T.1    Stormo, G.D.2
  • 23
    • 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., Rouzé,P. and Moreau,Y. (2001) A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics, 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    Rouzé, P.6    Moreau, Y.7
  • 24
    • 0001856084 scopus 로고
    • Optimization through evolution and recombination
    • Yovits,M.C., Jacobi,G.T. and Goldstein,G.D. (eds), Spartan Press, Washington, DC
    • Bremmerman,H.J. (1962) Optimization through evolution and recombination. In: Yovits,M.C., Jacobi,G.T. and Goldstein,G.D. (eds), Self-Organizing Systems. Spartan Press, Washington, DC.
    • (1962) Self-Organizing Systems
    • Bremmerman, H.J.1
  • 37
    • 0033954325 scopus 로고    scopus 로고
    • COMPEL: A database on composite regulatory elements providing combinatorial transcriptional regulation
    • Kel-Margoulis,O.V., Romashchenko,A.G., Kolchanov,N.A., Wingender,E. and Kel,A.E. (2000) COMPEL: a database on composite regulatory elements providing combinatorial transcriptional regulation. Nucleic Acids Res., 28, 311-315.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 311-315
    • Kel-Margoulis, O.V.1    Romashchenko, A.G.2    Kolchanov, N.A.3    Wingender, E.4    Kel, A.E.5
  • 38
    • 0029901640 scopus 로고    scopus 로고
    • Analysis of compositionally biased regions in sequence databases
    • Wootton,J.C. and Federhen,S. (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol., 266, 554-571.
    • (1996) Methods Enzymol. , vol.266 , pp. 554-571
    • Wootton, J.C.1    Federhen, S.2
  • 43
    • 0028971143 scopus 로고
    • MatInd and MatInspector: New fast and versatile tools for detection of consensus matches in nucleotide sequence data
    • Quandt,K., Frech,K., Karas,H., Wingender,E. and Werner,T. (1995) MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res., 23, 4878-4884.
    • (1995) Nucleic Acids Res. , vol.23 , pp. 4878-4884
    • Quandt, K.1    Frech, K.2    Karas, H.3    Wingender, E.4    Werner, T.5
  • 44
    • 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. Nat. Biotechnol., 20, 835-839.
    • (2002) Nat. Biotechnol. , vol.20 , pp. 835-839
    • Liu, X.S.1    Brutlag, D.L.2    Liu, J.S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.