메뉴 건너뛰기




Volumn 16, Issue 10, 1998, Pages 939-945

Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation

Author keywords

Functional genomics; Gene expression

Indexed keywords

GALACTOSE; GLUCOSE; HEAT SHOCK PROTEIN;

EID: 0031787969     PISSN: 10870156     EISSN: None     Source Type: Journal    
DOI: 10.1038/nbt1098-939     Document Type: Article
Times cited : (785)

References (45)
  • 1
    • 0030768943 scopus 로고    scopus 로고
    • Laboratory workhorse decoded
    • Pennisi, E. 1997. Laboratory workhorse decoded. Science 277:1432-1434.
    • (1997) Science , vol.277 , pp. 1432-1434
    • Pennisi, E.1
  • 4
    • 0029589284 scopus 로고
    • Five prompters integrate control of the cob/pdu regulon in Salmonella typhimurium
    • Chen, P., Ailion, M., Bobik, T., Stormo, G., and Roth, J. 1995. Five prompters integrate control of the cob/pdu regulon in Salmonella typhimurium. J. Bacteriol. 177:5401-5410.
    • (1995) J. Bacteriol. , vol.177 , pp. 5401-5410
    • Chen, P.1    Ailion, M.2    Bobik, T.3    Stormo, G.4    Roth, J.5
  • 5
    • 0027457409 scopus 로고
    • Global regulation of gene expression in Escherichia coli
    • Chuang, S.E., Daniels, D.L., and Blattner, F.R. 1993. Global regulation of gene expression in Escherichia coli. J. Bacteriol. 175:2026-2036.
    • (1993) J. Bacteriol. , vol.175 , pp. 2026-2036
    • Chuang, S.E.1    Daniels, D.L.2    Blattner, F.R.3
  • 6
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary UNA microarray
    • Schena, M., Shalon, D., Davis, R.W., and Brown, P.O. 1995. Quantitative monitoring of gene expression patterns with a complementary UNA 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
  • 8
    • 0029852580 scopus 로고    scopus 로고
    • Use of a cDNA microarray to analyse gene expression patterns in human cancer
    • DeRisi, J., Penland, L., Brown, P.O., Bittner, M.L., Meltzer, P.S., Ray, M. et al. 1996. Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat. Genet. 14:457-460.
    • (1996) Nat. Genet. , vol.14 , pp. 457-460
    • DeRisi, J.1    Penland, L.2    Brown, P.O.3    Bittner, M.L.4    Meltzer, P.S.5    Ray, M.6
  • 10
    • 0028961870 scopus 로고
    • Turnover mechanisms of the stable yeast PGK1 mRNA
    • Muhlrad, D., Decker, C.J., and Parker, R. 1995. Turnover mechanisms of the stable yeast PGK1 mRNA. Mol. Cell. Biol. 15:2145-2156.
    • (1995) Mol. Cell. Biol. , vol.15 , pp. 2145-2156
    • Muhlrad, D.1    Decker, C.J.2    Parker, R.3
  • 11
    • 0029973094 scopus 로고    scopus 로고
    • Interrelationships of the pathways of mRNA decay and translation in eukaryotlc cells
    • Jacobson, A. and Peltz, S.W. 1996. Interrelationships of the pathways of mRNA decay and translation in eukaryotlc cells. Annu. Rev. Biochem. 65:693-739.
    • (1996) Annu. Rev. Biochem. , vol.65 , pp. 693-739
    • Jacobson, A.1    Peltz, S.W.2
  • 12
    • 0030748996 scopus 로고    scopus 로고
    • Making (anti)sense of non-coding sequence conservation
    • Lipman, D.J. 1997. Making (anti)sense of non-coding sequence conservation. Nucleic Acids. Res. 25:3580-3583.
    • (1997) Nucleic Acids. Res. , vol.25 , pp. 3580-3583
    • Lipman, D.J.1
  • 13
    • 0030889152 scopus 로고    scopus 로고
    • Software for the analysis of DNA sequence elements of transcription
    • Frech, K., Quandt, K., and Werner, T. 1997. Software for the analysis of DNA sequence elements of transcription. CABIOS 13:89-97.
    • (1997) CABIOS , vol.13 , pp. 89-97
    • Frech, K.1    Quandt, K.2    Werner, T.3
  • 14
    • 0002759539 scopus 로고
    • Unsupervised learning of multiple motifs in biopolymers using expectation maximization
    • Bailey, T.L. and Elkan, C. 1995. Unsupervised learning of multiple motifs in biopolymers using expectation maximization. Machine Learning Journal 21:51-83.
    • (1995) Machine Learning Journal , vol.21 , pp. 51-83
    • Bailey, T.L.1    Elkan, C.2
  • 15
    • 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
  • 16
    • 0027912333 scopus 로고
    • Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment
    • Lawrence, C.E., Altschul, S.F., Boguskl, 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    Boguskl, M.S.3    Liu, J.S.4    Neuwald, A.F.5    Wootton, J.C.6
  • 17
    • 0029058555 scopus 로고
    • Transcriptional regulation in the yeast GAL gene family: A complex genetic network
    • Lohr, D., Venkov, P., and Zlatanova, J. 1995. Transcriptional regulation in the yeast GAL gene family: a complex genetic network. FASEB J. 9:777-787.
    • (1995) FASEB J. , vol.9 , pp. 777-787
    • Lohr, D.1    Venkov, P.2    Zlatanova, J.3
  • 18
    • 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
  • 19
    • 0026480852 scopus 로고
    • Histone H3 transcription in Saccharomyces cerevisiae is controlled by multiple cell cycle activation sites and a constitutive negative regulatory element
    • Freeman, K.B., Karns, L.R., Lutz, K.A., and Smith, M.M. 1992. Histone H3 transcription in Saccharomyces cerevisiae is controlled by multiple cell cycle activation sites and a constitutive negative regulatory element. Mol. Cell. Biol. 12:5455-5463.
    • (1992) Mol. Cell. Biol. , vol.12 , pp. 5455-5463
    • Freeman, K.B.1    Karns, L.R.2    Lutz, K.A.3    Smith, M.M.4
  • 20
    • 0025863511 scopus 로고
    • The regulation of histone synthesis in the cell cycle
    • Osley, M.A. 1991. The regulation of histone synthesis in the cell cycle. Annu. Rev. Biochem. 60:827-861.
    • (1991) Annu. Rev. Biochem. , vol.60 , pp. 827-861
    • Osley, M.A.1
  • 21
    • 0029655723 scopus 로고    scopus 로고
    • Start-specific transcription in yeast
    • Breeden, L. 1996. Start-specific transcription in yeast. Curr. Top. Microbiol. Immunol. 208:95-127.
    • (1996) Curr. Top. Microbiol. Immunol. , vol.208 , pp. 95-127
    • Breeden, L.1
  • 22
    • 0030977093 scopus 로고    scopus 로고
    • A novel Mem 1-dependent element in the SWI4, CLN3, CDC6, and CDC47 promoters activates M/G1 -specific transcription
    • Mclnerny, C.J., Partridge, J.F., Mikesell, G.E., Creemer, D.P., and Breeden, L.L. 1997. A novel Mem 1-dependent element in the SWI4, CLN3, CDC6, and CDC47 promoters activates M/G1 -specific transcription. Genes Dev. 11:1277-1288.
    • (1997) Genes Dev. , vol.11 , pp. 1277-1288
    • Mclnerny, C.J.1    Partridge, J.F.2    Mikesell, G.E.3    Creemer, D.P.4    Breeden, L.L.5
  • 23
    • 0001225813 scopus 로고
    • Mating-type determination and mating-type interconversion in Saccharomyces cerevisiae
    • Jones, E.W., Pringle, J.R., and Broach, J.R. (eds.). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
    • Herskowitz, I., Rine, J., and Strathern, J. 1992. Mating-type determination and mating-type interconversion in Saccharomyces cerevisiae, pp. 583-656, in Gene expression, Vol. 2. Jones, E.W., Pringle, J.R., and Broach, J.R. (eds.). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
    • (1992) Gene Expression , vol.2 , pp. 583-656
    • Herskowitz, I.1    Rine, J.2    Strathern, J.3
  • 24
    • 0000632439 scopus 로고
    • Regulation of carbon and phosphate utilization
    • Jones, E.W., Prlngie, J.R., and Broach, J.R. (eds.). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
    • Johnston, M. and Carison, M. 1992. Regulation of carbon and phosphate utilization, pp. 193-281 in Gene expression, Vol. 2. Jones, E.W., Prlngie, J.R., and Broach, J.R. (eds.). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
    • (1992) Gene Expression , vol.2 , pp. 193-281
    • Johnston, M.1    Carison, M.2
  • 25
    • 0001086085 scopus 로고
    • The heat-shock response of Saccnaromyces cerevisiae
    • Jones, E.W., Pringle, J.R., and Broach, J.R. (eds.). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
    • Craig, E.A. 1992. The heat-shock response of Saccnaromyces cerevisiae, pp. 501-537, in Gene expression, Vol. 2. Jones, E.W., Pringle, J.R., and Broach, J.R. (eds.). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
    • (1992) Gene Expression , vol.2 , pp. 501-537
    • Craig, E.A.1
  • 26
    • 0030003064 scopus 로고    scopus 로고
    • Msn2p, a zinc finger DNA-binding protein, is the transcriptional activator of the multistress response in Saccharomyces cerevisiae
    • Schmitt, A.P. and McEntee, K. 1996. Msn2p, a zinc finger DNA-binding protein, is the transcriptional activator of the multistress response in Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. USA 93:5777-5782.
    • (1996) Proc. Natl. Acad. Sci. USA , vol.93 , pp. 5777-5782
    • Schmitt, A.P.1    McEntee, K.2
  • 27
    • 0027509063 scopus 로고
    • Heat shock-mediated cell cycle blockage and G1 cyclin expression in the yeast Saccnaromyces cerevisiae
    • Rowley, A., Johnston, G.C., Butler, B., Werner-Washburne, M. and Singer, R.A. 1993. Heat shock-mediated cell cycle blockage and G1 cyclin expression in the yeast Saccnaromyces cerevisiae. Mol. Cell. Biol. 13:1034-1041.
    • (1993) Mol. Cell. Biol. , vol.13 , pp. 1034-1041
    • Rowley, A.1    Johnston, G.C.2    Butler, B.3    Werner-Washburne, M.4    Singer, R.A.5
  • 28
    • 0027331505 scopus 로고
    • How do "Zn2 cys6" proteins distinguish between similar upstream activation sites? Comparison of the DNA-blnding specificity of the GAL4 protein in vitro and in vivo
    • Vashee, S., Xu, H., Johnston, S.A., and Kodadek, T. 1993. How do "Zn2 cys6" proteins distinguish between similar upstream activation sites? Comparison of the DNA-blnding specificity of the GAL4 protein in vitro and in vivo. J. Biol. Chem. 268:24699-24706.
    • (1993) J. Biol. Chem. , vol.268 , pp. 24699-24706
    • Vashee, S.1    Xu, H.2    Johnston, S.A.3    Kodadek, T.4
  • 30
    • 0029083543 scopus 로고
    • Response of a yeast glycogen synthase gene to stress
    • NI, H.T. and LaPorte, D.C. 1995. Response of a yeast glycogen synthase gene to stress. Mol. Microbiol. 16:1197-1205.
    • (1995) Mol. Microbiol. , vol.16 , pp. 1197-1205
    • Ni, H.T.1    LaPorte, D.C.2
  • 31
    • 0001134626 scopus 로고
    • Pheromone response and signal transduction during the mating process of Saccharomyces cerevisiae
    • Jones, E.W., Pringle, J.R., and Broach, J.R. (eds.). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
    • Sprague, G.F. and Thorner, J.W. 1992. Pheromone response and signal transduction during the mating process of Saccharomyces cerevisiae, pp. 657-744, in Gene expression, Vol. 2. Jones, E.W., Pringle, J.R., and Broach, J.R. (eds.). Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
    • (1992) Gene Expression , vol.2 , pp. 657-744
    • Sprague, G.F.1    Thorner, J.W.2
  • 33
    • 0028794516 scopus 로고
    • Construction of a set of convenient Saccnaromyces cerevisiae strains that are isogenic to S288C
    • Winston, F., Dollard, C., and Ricupero-Hovasse, S.L. 1995. Construction of a set of convenient Saccnaromyces cerevisiae strains that are isogenic to S288C. Yeast 11:53-55.
    • (1995) Yeast , vol.11 , pp. 53-55
    • Winston, F.1    Dollard, C.2    Ricupero-Hovasse, S.L.3
  • 35
    • 0020264211 scopus 로고
    • Quantitative analysis of the heat shock response of Saccnaromyces cerevisiae
    • Miller, M.J., Xuong, N.H., and Geiduschek, E.P. 1982. Quantitative analysis of the heat shock response of Saccnaromyces cerevisiae. J. Bacteriol. 151:311-327.
    • (1982) J. Bacteriol. , vol.151 , pp. 311-327
    • Miller, M.J.1    Xuong, N.H.2    Geiduschek, E.P.3
  • 36
    • 0028964292 scopus 로고
    • PDA1 mRNA; a standard for quantitation of mRNA in Saccharomyces cerevisiae superior to ACT1 mRNA
    • Wenzel, T.J., Teunissen, A.W., and de Steensma, H.Y. 1995. PDA1 mRNA; a standard for quantitation of mRNA in Saccharomyces cerevisiae superior to ACT1 mRNA. Nucleic Acids Res. 23:883-884.
    • (1995) Nucleic Acids Res. , vol.23 , pp. 883-884
    • Wenzel, T.J.1    Teunissen, A.W.2    De Steensma, H.Y.3
  • 37
    • 0023147228 scopus 로고
    • Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters
    • Berg, O.G. and von Hippel, P.H. 1987. Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol. 193:723-750.
    • (1987) J. Mol. Biol. , vol.193 , pp. 723-750
    • Berg, O.G.1    Von Hippel, P.H.2
  • 38
    • 84950424966 scopus 로고
    • Bayeslan models for multiple local sequence alignment and Gibbs sampling strategies
    • Liu, J.S., Neuwald, A.F., and Lawrence, C.E. 1995. Bayeslan models for multiple local sequence alignment and Gibbs sampling strategies. J. Amer. Stat. Assoc. 90:1153-1170.
    • (1995) J. Amer. Stat. Assoc. , vol.90 , pp. 1153-1170
    • Liu, J.S.1    Neuwald, A.F.2    Lawrence, C.E.3
  • 39
    • 85081421864 scopus 로고    scopus 로고
    • http://arep.med.harvard.edu/mrnadata.
  • 40
    • 0030861819 scopus 로고    scopus 로고
    • TRANSFAC, TRRD and COMPEL: Towards a federated database system on transcriptional regulation
    • Wingender, E., Keli, A.E., Kel, O.V., Karas, H., Heinemeyer, T et al. 1997. TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation. Nucleic Acids Res. 25:265-268.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 265-268
    • Wingender, E.1    Keli, A.E.2    Kel, O.V.3    Karas, H.4    Heinemeyer, T.5
  • 41
    • 0028971143 scopus 로고
    • Matlnd and matinspector: New fast and versatile tools for detection of consensus matches in nucledtide sequence data
    • Quandt, K., Frech, K., Karas, H., Wingender, E., and Werner, T. 1995. Matlnd and matinspector: new fast and versatile tools for detection of consensus matches in nucledtide 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
  • 42
    • 0023649578 scopus 로고
    • A germline transformation analysis reveals flexibility in the organization of heat shock consensus elements
    • Simon, J.A. and Lis, J.T. 1987. A germline transformation analysis reveals flexibility in the organization of heat shock consensus elements. Nucleic Acids Res. 15:2971-2988.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 2971-2988
    • Simon, J.A.1    Lis, J.T.2
  • 43
    • 0028106363 scopus 로고
    • The HOG pathway controls osmotic regulation of transcription via the stress response element (STRE) of the Saccharomyces cerevisiae CTT1 gene
    • Schuller, C., Brewster, J.L., Alexander, M.R., Gustin, M.C., and Ruis, H. 1994. The HOG pathway controls osmotic regulation of transcription via the stress response element (STRE) of the Saccharomyces cerevisiae CTT1 gene. EMBO J. 13:4382-4389.
    • (1994) EMBO J. , vol.13 , pp. 4382-4389
    • Schuller, C.1    Brewster, J.L.2    Alexander, M.R.3    Gustin, M.C.4    Ruis, H.5
  • 44
    • 0029879360 scopus 로고    scopus 로고
    • The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE)
    • Martinez-Pastor, M.T., Marchler, G., Schuller, C., Marchler-Bauer, A., Ruis, H. et al. 1996. The Saccharomyces cerevisiae zinc finger proteins Msn2p and Msn4p are required for transcriptional induction through the stress response element (STRE). EMBO J. 15:2227-2235.
    • (1996) EMBO J. , vol.15 , pp. 2227-2235
    • Martinez-Pastor, M.T.1    Marchler, G.2    Schuller, C.3    Marchler-Bauer, A.4    Ruis, H.5
  • 45
    • 0031837058 scopus 로고    scopus 로고
    • Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E
    • Tevazoie, S. and Church, G.M. 1998. Quantitative whole-genome analysis of DNA-protein interactions by in vivo methylase protection in E. coli. Nat. Biotechnol. 16:566-571.
    • (1998) Coli. Nat. Biotechnol. , vol.16 , pp. 566-571
    • Tevazoie, S.1    Church, G.M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.