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Volumn 36, Issue 12, 2004, Pages 1331-1339

Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays

Author keywords

[No Author keywords available]

Indexed keywords

CIS ACTING ELEMENT; DNA; RAP PROTEIN; RAP1 PROTEIN; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR ABF 1; TRANSCRIPTION FACTOR MIG 1; UNCLASSIFIED DRUG;

EID: 9644268153     PISSN: 10614036     EISSN: None     Source Type: Journal    
DOI: 10.1038/ng1473     Document Type: Article
Times cited : (308)

References (49)
  • 1
    • 0028806048 scopus 로고
    • Quantitative monitoring of gene expression patterns with a complementary DNA microarray
    • Schena, M., Shalon, D., Davis, R.W. & Brown, P.O. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467-470 (1995).
    • (1995) Science , vol.270 , pp. 467-470
    • Schena, M.1    Shalon, D.2    Davis, R.W.3    Brown, P.O.4
  • 3
    • 0034704248 scopus 로고    scopus 로고
    • Genome-wide location and function of DNA binding proteins
    • Ren, B. et al. Genome-wide location and function of DNA binding proteins. Science 290, 2306-2309 (2000).
    • (2000) Science , vol.290 , pp. 2306-2309
    • Ren, B.1
  • 4
    • 0035945567 scopus 로고    scopus 로고
    • Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF
    • Iyer, V.R. et al. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533-538 (2001).
    • (2001) Nature , vol.409 , pp. 533-538
    • Iyer, V.R.1
  • 5
    • 0034934774 scopus 로고    scopus 로고
    • Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association
    • Lieb, J.D., Liu, X., Botstein, D. & Brown, P.O. Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat. Genet. 28, 327-334 (2001).
    • (2001) Nat. Genet. , vol.28 , pp. 327-334
    • Lieb, J.D.1    Liu, X.2    Botstein, D.3    Brown, P.O.4
  • 6
    • 0037174671 scopus 로고    scopus 로고
    • Transcriptional regulatory networks in Saccharomyces cerevisiae
    • Lee, T. et al. Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298, 799-804 (2002).
    • (2002) Science , vol.298 , pp. 799-804
    • Lee, T.1
  • 7
    • 0034628508 scopus 로고    scopus 로고
    • A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
    • Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627 (2000).
    • (2000) Nature , vol.403 , pp. 623-627
    • Uetz, P.1
  • 8
    • 0034622925 scopus 로고    scopus 로고
    • Printing proteins as microarrays for high-throughput function determination
    • MacBeath, G. & Schreiber, S.L. Printing proteins as microarrays for high-throughput function determination. Science 289, 1760-1763 (2000).
    • (2000) Science , vol.289 , pp. 1760-1763
    • MacBeath, G.1    Schreiber, S.L.2
  • 9
    • 0033974688 scopus 로고    scopus 로고
    • Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins
    • Ito, T. et al. Toward a protein-protein interaction map of the budding yeast: A comprehensive system to examine two-hybrid interactions in all possible combinations between the yeast proteins. Proc. Natl. Acad. Sci. USA 97, 1143-1147 (2000).
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 1143-1147
    • Ito, T.1
  • 10
    • 0037050004 scopus 로고    scopus 로고
    • Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry
    • Ho, Y. et al. Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415, 180-183 (2002).
    • (2002) Nature , vol.415 , pp. 180-183
    • Ho, Y.1
  • 11
    • 0035912721 scopus 로고    scopus 로고
    • Exploring the DNA-binding specificities of zinc fingers with DNA microarrays
    • Bulyk, M.L., Huang, X., Choo, Y. & Church, G.M. Exploring the DNA-binding specificities of zinc fingers with DNA microarrays. Proc. Natl. Acad. Sci. USA 98, 7158-7163 (2001).
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 7158-7163
    • Bulyk, M.L.1    Huang, X.2    Choo, Y.3    Church, G.M.4
  • 12
    • 2342507824 scopus 로고    scopus 로고
    • Quantitative high-throughput analysis of transcription factor binding specificities
    • Linnell, J. et al. Quantitative high-throughput analysis of transcription factor binding specificities. Nucleic Acids Res. 32, e44 (2004).
    • (2004) Nucleic Acids Res. , vol.32
    • Linnell, J.1
  • 13
    • 0031407447 scopus 로고    scopus 로고
    • Regulation of ribosome synthesis in yeast
    • Planta, R.J. Regulation of ribosome synthesis in yeast. Yeast 13, 1505-1518 (1997).
    • (1997) Yeast , vol.13 , pp. 1505-1518
    • Planta, R.J.1
  • 14
    • 0029963828 scopus 로고    scopus 로고
    • The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA
    • Konig, P., Giraldo, R., Chapman, L. & Rhodes, D. The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA. Cell 85, 125-136 (1996).
    • (1996) Cell , vol.85 , pp. 125-136
    • Konig, P.1    Giraldo, R.2    Chapman, L.3    Rhodes, D.4
  • 15
    • 0031761689 scopus 로고    scopus 로고
    • Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae
    • Lutfiyya, L.L. et al. Characterization of three related glucose repressors and genes they regulate in Saccharomyces cerevisiae. Genetics 150, 1377-1391 (1998).
    • (1998) Genetics , vol.150 , pp. 1377-1391
    • Lutfiyya, L.L.1
  • 16
    • 0035228215 scopus 로고    scopus 로고
    • BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes
    • Liu, X., Brutlag, D. & Liu, J. BioProspector: discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput. 2001, 127-138 (2001).
    • (2001) Pac. Symp. Biocomput. , vol.2001 , pp. 127-138
    • Liu, X.1    Brutlag, D.2    Liu, J.3
  • 17
    • 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. & Church, G.M. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J. Mol. Biol. 296, 1205-1214 (2000).
    • (2000) J. Mol. Biol. , vol.296 , pp. 1205-1214
    • Hughes, J.D.1    Estep, P.W.2    Tavazoie, S.3    Church, G.M.4
  • 18
    • 0033976586 scopus 로고    scopus 로고
    • TRANSFAC: An integrated system for gene expression regulation
    • Wingender, E. et al. TRANSFAC: an integrated system for gene expression regulation. Nucleic Acids Res. 28, 316-319 (2000).
    • (2000) Nucleic Acids Res. , vol.28 , pp. 316-319
    • Wingender, E.1
  • 19
    • 0038349948 scopus 로고    scopus 로고
    • Sequencing and comparison of yeast species to identify genes and regulatory elements
    • Kellis, M., Patterson, N., Endrizzi, M., Birren, B. & Lander, E. Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 423, 241-254 (2003).
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.5
  • 20
    • 0038724989 scopus 로고    scopus 로고
    • Finding functional features in Saccharomyces genomes by phylogenetic footprinting
    • Cliften, P. et al. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 301, 71-76 (2003).
    • (2003) Science , vol.301 , pp. 71-76
    • Cliften, P.1
  • 21
    • 0032573426 scopus 로고    scopus 로고
    • A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome
    • Robison, K., McGuire, A.M. & Church, G.M. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome. J. Mol. Biol. 284, 241-254 (1998).
    • (1998) J. Mol. Biol. , vol.284 , pp. 241-254
    • Robison, K.1    McGuire, A.M.2    Church, G.M.3
  • 22
    • 0033028596 scopus 로고    scopus 로고
    • Systematic determination of genetic network architecture
    • Tavazoie, S., Hughes, J., Campbell, M., Cho, R. & Church, G. Systematic determination of genetic network architecture. Nat. Genet. 22, 281-285 (1999).
    • (1999) Nat. Genet. , vol.22 , pp. 281-285
    • Tavazoie, S.1    Hughes, J.2    Campbell, M.3    Cho, R.4    Church, G.5
  • 23
    • 0035817637 scopus 로고    scopus 로고
    • A protein interaction map for cell polarity development
    • Drees, B.L. et al. A protein interaction map for cell polarity development. J. Cell. Biol. 154, 549-571 (2001).
    • (2001) J. Cell. Biol. , vol.154 , pp. 549-571
    • Drees, B.L.1
  • 24
    • 1942453302 scopus 로고    scopus 로고
    • Predicting gene expression from sequence
    • Beer, M.A. & Tavazoie, S. Predicting gene expression from sequence. Cell 117, 185-198 (2004).
    • (2004) Cell , vol.117 , pp. 185-198
    • Beer, M.A.1    Tavazoie, S.2
  • 25
    • 0033821210 scopus 로고    scopus 로고
    • Cooperative regulation of DOG2, encoding 2-deoxyglucose-6-phosphate phosphatase, by Snf1 kinase and the high-osmolarity glycerol-mitogen-activated protein kinase cascade in stress responses of Saccharomyces cerevisiae
    • Tsujimoto, Y., Izawa, S. & Inoue, Y. Cooperative regulation of DOG2, encoding 2-deoxyglucose-6-phosphate phosphatase, by Snf1 kinase and the high-osmolarity glycerol-mitogen-activated protein kinase cascade in stress responses of Saccharomyces cerevisiae. J. Bacteriol. 182, 5121-5126 (2000).
    • (2000) J. Bacteriol. , vol.182 , pp. 5121-5126
    • Tsujimoto, Y.1    Izawa, S.2    Inoue, Y.3
  • 26
    • 0035477582 scopus 로고    scopus 로고
    • Regulatory elements in the FBP1 promoter respond differently to glucose-dependent signals in Saccharomyces cerevisiae
    • Zaragoza, O., Vincent, O. & Gancedo, J.M. Regulatory elements in the FBP1 promoter respond differently to glucose-dependent signals in Saccharomyces cerevisiae. Biochem. J. 359, 193-201 (2001).
    • (2001) Biochem. J. , vol.359 , pp. 193-201
    • Zaragoza, O.1    Vincent, O.2    Gancedo, J.M.3
  • 27
    • 0025996980 scopus 로고
    • Regulated expression of the GAL4 activator gene in yeast provides a sensitive genetic switch for glucose repression
    • Griggs, D.W. & Johnston, M. Regulated expression of the GAL4 activator gene in yeast provides a sensitive genetic switch for glucose repression. Proc. Natl. Acad. Sci. USA 88, 8597-8601 (1991).
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 8597-8601
    • Griggs, D.W.1    Johnston, M.2
  • 28
    • 0033571212 scopus 로고    scopus 로고
    • Expression of GUT1, which encodes glycerol kinase in Saccharomyces cerevisiae, is controlled by the positive regulators Adr1p, Ino2p and Ino4p and the negative regulator Opi1p in a carbon source-dependent fashion
    • Grauslund, M., Lopes, J.M. & Ronnow, B. Expression of GUT1, which encodes glycerol kinase in Saccharomyces cerevisiae, is controlled by the positive regulators Adr1p, Ino2p and Ino4p and the negative regulator Opi1p in a carbon source-dependent fashion. Nucleic Acids Res. 27, 4391-4398 (1999).
    • (1999) Nucleic Acids Res. , vol.27 , pp. 4391-4398
    • Grauslund, M.1    Lopes, J.M.2    Ronnow, B.3
  • 29
    • 0032865543 scopus 로고    scopus 로고
    • Function and regulation of yeast hexose transporters
    • Ozcan, S. & Johnston, M. Function and regulation of yeast hexose transporters. Microbiol. Mol. Biol. Rev. 63, 554-569 (1999).
    • (1999) Microbiol. Mol. Biol. Rev. , vol.63 , pp. 554-569
    • Ozcan, S.1    Johnston, M.2
  • 30
    • 0033390344 scopus 로고    scopus 로고
    • Cat8p the activator of gluconeogenic genes in Saccharomyces cerevisiae, regulates carbon source-dependent expression of NADP-dependent cytosolic isocitrate dehydrogenase (Idp2p) and lactate permease (Jen1p)
    • Bojunga, N. & Entian, K.D. Cat8p the activator of gluconeogenic genes in Saccharomyces cerevisiae, regulates carbon source-dependent expression of NADP-dependent cytosolic isocitrate dehydrogenase (Idp2p) and lactate permease (Jen1p). Mol. Gen. Genet. 262, 869-875 (1999).
    • (1999) Mol. Gen. Genet. , vol.262 , pp. 869-875
    • Bojunga, N.1    Entian, K.D.2
  • 31
    • 0030953974 scopus 로고    scopus 로고
    • The Snf1 protein kinase and its activating subunit, Snf4, interact with distinct domains of the Sip1/Sip2/Gal83 component in the kinase complex
    • Jiang, R. & Carlson, M. The Snf1 protein kinase and its activating subunit, Snf4, interact with distinct domains of the Sip1/Sip2/Gal83 component in the kinase complex. Mol. Cell. Biol. 17, 2099-2106 (1997).
    • (1997) Mol. Cell. Biol. , vol.17 , pp. 2099-2106
    • Jiang, R.1    Carlson, M.2
  • 32
    • 0036067136 scopus 로고    scopus 로고
    • Depression of Saccharomyces cerevisiae invasive growth on non-glucose carbon sources requires the Snf1 kinase
    • Palecek, S.P., Parikh, A.S., Huh, J.H. & Kron, S.J. Depression of Saccharomyces cerevisiae invasive growth on non-glucose carbon sources requires the Snf1 kinase. Mol. Microbiol. 45, 453-469 (2002).
    • (2002) Mol. Microbiol. , vol.45 , pp. 453-469
    • Palecek, S.P.1    Parikh, A.S.2    Huh, J.H.3    Kron, S.J.4
  • 33
    • 2442543114 scopus 로고    scopus 로고
    • Analysis of complementary expression profiles following WT1 induction versus repression reveals the cholesterol/fatty acid synthetic pathways as a possible major target of WT1
    • Rae, F.K. et al. Analysis of complementary expression profiles following WT1 induction versus repression reveals the cholesterol/fatty acid synthetic pathways as a possible major target of WT1. Oncogene 23, 3067-3079 (2004).
    • (2004) Oncogene , vol.23 , pp. 3067-3079
    • Rae, F.K.1
  • 34
    • 4544352942 scopus 로고    scopus 로고
    • Transcriptional regulatory code of a eukaryotic genome
    • Harbison, CT. et al. Transcriptional regulatory code of a eukaryotic genome. Nature 431, 99-104 (2004).
    • (2004) Nature , vol.431 , pp. 99-104
    • Harbison, C.T.1
  • 35
    • 0036366689 scopus 로고    scopus 로고
    • Combining location and expression data for principled discovery of genetic regulatory network models
    • Hartemink, A., Gifford, D., Jaakkola, T. & Young, R. Combining location and expression data for principled discovery of genetic regulatory network models. Pac. Symp. Biocomput. 2002, 437-449 (2002).
    • (2002) Pac. Symp. Biocomput. , vol.2002 , pp. 437-449
    • Hartemink, A.1    Gifford, D.2    Jaakkola, T.3    Young, R.4
  • 36
    • 18344365585 scopus 로고    scopus 로고
    • Novel fluorescence labeling and high-throughput assay technologies for in vitro analysis of protein interactions
    • Doi, N. et al. Novel fluorescence labeling and high-throughput assay technologies for in vitro analysis of protein interactions. Genome Res. 12, 487-492 (2002).
    • (2002) Genome Res. , vol.12 , pp. 487-492
    • Doi, N.1
  • 37
    • 0035875327 scopus 로고    scopus 로고
    • Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay
    • Man, T.K. & Stormo, G.D. Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic Acids Res. 29, 2471-2478 (2001).
    • (2001) Nucleic Acids Res. , vol.29 , pp. 2471-2478
    • Man, T.K.1    Stormo, G.D.2
  • 38
    • 0036493201 scopus 로고    scopus 로고
    • Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors
    • Bulyk, M., Johnson, P. & Church, G. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res. 30, 1255-1261 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. 1255-1261
    • Bulyk, M.1    Johnson, P.2    Church, G.3
  • 40
    • 0026742626 scopus 로고
    • Toward rules relating zinc finger protein sequences and DNA binding site preferences
    • Desjarlais, J.R. & Berg, J.M. Toward rules relating zinc finger protein sequences and DNA binding site preferences. Proc. Natl. Acad. Sci. USA 89, 7345-7349 (1992).
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 7345-7349
    • Desjarlais, J.R.1    Berg, J.M.2
  • 41
    • 9644283155 scopus 로고    scopus 로고
    • ModuleFinder: A tool for computational discovery of cis regulatory modules
    • in the press
    • Philippakis, A., He, F. & Bulyk, M. ModuleFinder: a tool for computational discovery of cis regulatory modules. Pac. Symp. Biocomput (in the press).
    • Pac. Symp. Biocomput
    • Philippakis, A.1    He, F.2    Bulyk, M.3
  • 42
    • 0035860499 scopus 로고    scopus 로고
    • Global analysis of protein activities using proteome chips
    • Zhu, H. et al. Global analysis of protein activities using proteome chips. Science 26, 2101-2105 (2001).
    • (2001) Science , vol.26 , pp. 2101-2105
    • Zhu, H.1
  • 43
    • 0037188477 scopus 로고    scopus 로고
    • Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range
    • Dudley, A., Aach, J., Steffen, M. & Church, G. Measuring absolute expression with microarrays with a calibrated reference sample and an extended signal intensity range. Proc. Natl. Acad. Sci. USA 99, 7554-7559 (2002).
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 7554-7559
    • Dudley, A.1    Aach, J.2    Steffen, M.3    Church, G.4
  • 44
    • 84947318637 scopus 로고
    • Locally weighted regression: An approach to regression analysis by local fitting
    • Cleveland, W. & Devlin, S. Locally weighted regression: An approach to regression analysis by local fitting. J. Am. Stat. Assoc. 83, 596-610 (1988).
    • (1988) J. Am. Stat. Assoc. , vol.83 , pp. 596-610
    • Cleveland, W.1    Devlin, S.2
  • 46
    • 0036324753 scopus 로고    scopus 로고
    • An algorithm for finding protein - DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments
    • Liu, X., Brutlag, D. & Liu, J. An algorithm for finding protein - DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol. 20, 835-839 (2002).
    • (2002) Nat. Biotechnol. , vol.20 , pp. 835-839
    • Liu, X.1    Brutlag, D.2    Liu, J.3
  • 48
    • 0141993704 scopus 로고    scopus 로고
    • A gene-coexpression network for global discovery of conserved genetic modules
    • Stuart, J.M., Segal, E., Koller, D. & Kim, S.K. A gene-coexpression network for global discovery of conserved genetic modules. Science 302, 249-255 (2003).
    • (2003) Science , vol.302 , pp. 249-255
    • Stuart, J.M.1    Segal, E.2    Koller, D.3    Kim, S.K.4
  • 49
    • 0025008168 scopus 로고
    • Sequence logos: A new way to display consensus sequences
    • Schneider, T.D. & Stephens, R.M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 18, 6097-6100 (1990).
    • (1990) Nucleic Acids Res. , vol.18 , pp. 6097-6100
    • Schneider, T.D.1    Stephens, R.M.2


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