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Volumn 24, Issue 13, 2008, Pages

Combinatorial influence of environmental parameters on transcription factor activity

Author keywords

[No Author keywords available]

Indexed keywords

CARBON; NITROGEN; OXYGEN; TRANSCRIPTION FACTOR;

EID: 46249094888     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn155     Document Type: Article
Times cited : (8)

References (40)
  • 1
    • 0034069495 scopus 로고    scopus 로고
    • Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium
    • Ashburner,M. et al. (2000) Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet., 25, 25-29.
    • (2000) Nat. Genet , vol.25 , pp. 25-29
    • Ashburner, M.1
  • 2
    • 33745449162 scopus 로고    scopus 로고
    • Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast
    • Balaji,S. et al. (2006) Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. J. Mol. Biol., 360, 213-227.
    • (2006) J. Mol. Biol , vol.360 , pp. 213-227
    • Balaji, S.1
  • 3
    • 18244389201 scopus 로고    scopus 로고
    • Standardizing global gene expression analysis between laboratories and across platforms
    • Bammler,T. et al. (2005) Standardizing global gene expression analysis between laboratories and across platforms. Nat. Methods, 2, 351-356.
    • (2005) Nat. Methods , vol.2 , pp. 351-356
    • Bammler, T.1
  • 4
    • 10744226222 scopus 로고    scopus 로고
    • Computational discovery of gene modules and regulatory networks
    • Bar-Joseph,Z. et al. (2003) Computational discovery of gene modules and regulatory networks. Nat. Biotechnol., 21, 1337-1342.
    • (2003) Nat. Biotechnol , vol.21 , pp. 1337-1342
    • Bar-Joseph, Z.1
  • 5
    • 0030979616 scopus 로고    scopus 로고
    • Met31p and met32p, two related zinc finger proteins, are involved in transcriptional regulation of yeast sulfur notion acid metabolism
    • Blaiseau,P.L. et al. (1997) Met31p and met32p, two related zinc finger proteins, are involved in transcriptional regulation of yeast sulfur notion acid metabolism. Mol. Cell Biol., 17, 3640-3648.
    • (1997) Mol. Cell Biol , vol.17 , pp. 3640-3648
    • Blaiseau, P.L.1
  • 6
    • 21644460849 scopus 로고    scopus 로고
    • Contribution of the saccharomyces cerevisiae transcriptional regulator leu3p to physiology and gene expression in nitrogen- and carbon-limited chemostat cultures
    • Boer,V.M. et al. (2005) Contribution of the saccharomyces cerevisiae transcriptional regulator leu3p to physiology and gene expression in nitrogen- and carbon-limited chemostat cultures. FEMS Yeast Res., 5, 885-897.
    • (2005) FEMS Yeast Res , vol.5 , pp. 885-897
    • Boer, V.M.1
  • 7
    • 34249063573 scopus 로고    scopus 로고
    • Transcriptional responses of saccharomyces cerevisiae to preferred and nonpreferred nitrogen sources in glucose-limited chemostat cultures
    • Boer,V.M. et al. (2007) Transcriptional responses of saccharomyces cerevisiae to preferred and nonpreferred nitrogen sources in glucose-limited chemostat cultures. FEMS Yeast Res., 7, 604-620.
    • (2007) FEMS Yeast Res , vol.7 , pp. 604-620
    • Boer, V.M.1
  • 8
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • Bolsta,AB.M. et al. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19, 185-193.
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolsta, A.M.1
  • 9
    • 33747813561 scopus 로고    scopus 로고
    • The inferelator: An algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
    • Bonneau,R. et al. (2006) The inferelator: An algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol., 7, R36.
    • (2006) Genome Biol , vol.7
    • Bonneau, R.1
  • 10
    • 0035135420 scopus 로고    scopus 로고
    • Regulatory element detection using correlation with expression
    • Bussemaker,H.J. et al. (2001) Regulatory element detection using correlation with expression. Nat. Genet., 27, 167-171.
    • (2001) Nat. Genet , vol.27 , pp. 167-171
    • Bussemaker, H.J.1
  • 11
    • 34247630099 scopus 로고    scopus 로고
    • Growth control of the eukaryote cell: A systems biology study in yeast
    • Castrillo,J. et al. (2007) Growth control of the eukaryote cell: A systems biology study in yeast. J. Biol., 6, 4.
    • (2007) J. Biol , vol.6 , pp. 4
    • Castrillo, J.1
  • 12
    • 33748694308 scopus 로고    scopus 로고
    • Identification of transcription factor cooperativity via stochastic system model
    • Chang,Y.-H. et al. (2006) Identification of transcription factor cooperativity via stochastic system model. Bioinformatics, 22 2276-2282.
    • (2006) Bioinformatics , vol.22 , pp. 2276-2282
    • Chang, Y.-H.1
  • 13
    • 9244257298 scopus 로고    scopus 로고
    • Interacting models of cooperative gene regulation
    • Das,D. et al. (2004) Interacting models of cooperative gene regulation. Proc. Natl Acad. Sci. USA, 101, 16234-16239.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 16234-16239
    • Das, D.1
  • 14
    • 0024713582 scopus 로고
    • Identification and characterization of hap4: A third component of the ccaat-bound hap2/hap3 heteromer
    • Forsburg,S.L. and Guarente,L. (1989) Identification and characterization of hap4: A third component of the ccaat-bound hap2/hap3 heteromer. Genes Dev., 3, 1166-1178.
    • (1989) Genes Dev , vol.3 , pp. 1166-1178
    • Forsburg, S.L.1    Guarente, L.2
  • 15
    • 2942582468 scopus 로고    scopus 로고
    • Defining transcriptional networks through integrative modeling of mrNA expression and transcription factor binding data
    • Gao,R et al. (2004) Defining transcriptional networks through integrative modeling of mrNA expression and transcription factor binding data. BMC Bioinformatics, 5, 31.
    • (2004) BMC Bioinformatics , vol.5 , pp. 31
    • Gao, R.1
  • 16
    • 4544352942 scopus 로고    scopus 로고
    • Transcriptional regulatory code of a eukaryotic genome
    • Harbison,C.T. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
    • (2004) Nature , vol.431 , pp. 99-104
    • Harbison, C.T.1
  • 17
    • 0032750741 scopus 로고    scopus 로고
    • Nitrogen catabolite repression in saccharomyces cerevisiae
    • Hofman-Bang,J. (1999) Nitrogen catabolite repression in saccharomyces cerevisiae. Mol. Biotechnol., 12, 35-73.
    • (1999) Mol. Biotechnol , vol.12 , pp. 35-73
    • Hofman-Bang, J.1
  • 18
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • Irizarry,R.A. et al. (2003) Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics, 4, 249-264.
    • (2003) Biostatistics , vol.4 , pp. 249-264
    • Irizarry, R.A.1
  • 19
    • 0025123264 scopus 로고
    • Reb1, a yeast DNA-binding protein with many targets, is essential for growth and bears some resemblance to the oncogene myb
    • Ju,Q.D. et al. (1990) Reb1, a yeast DNA-binding protein with many targets, is essential for growth and bears some resemblance to the oncogene myb. Mol. Cell Biol., 10, 5226-5234.
    • (1990) Mol. Cell Biol , vol.10 , pp. 5226-5234
    • Ju, Q.D.1
  • 20
    • 33847184205 scopus 로고    scopus 로고
    • Exploiting combinatorial cultivation conditions to infer transcriptional regulation
    • Knijnenburg,T.A. et al. (2007) Exploiting combinatorial cultivation conditions to infer transcriptional regulation. BMC Genomics, 8, 25.
    • (2007) BMC Genomics , vol.8 , pp. 25
    • Knijnenburg, T.A.1
  • 21
    • 0023768278 scopus 로고
    • Rox1 encodes a heme-induced repression factor regulating anb1 and cyc7 of sarcharomyces cerevisiae
    • Lowry,C.V. and Zitomer,R.S. (1988) Rox1 encodes a heme-induced repression factor regulating anb1 and cyc7 of sarcharomyces cerevisiae. Mol. Cell Biol., 8, 4651-4658.
    • (1988) Mol. Cell Biol , vol.8 , pp. 4651-4658
    • Lowry, C.V.1    Zitomer, R.S.2
  • 22
    • 4644326931 scopus 로고    scopus 로고
    • Genomic analysis of regulatory network dynamics reveals large topological changes
    • Luscombe,N.M. et al. (2004) Genomic analysis of regulatory network dynamics reveals large topological changes. Nature, 431, 308-312.
    • (2004) Nature , vol.431 , pp. 308-312
    • Luscombe, N.M.1
  • 23
    • 33645769260 scopus 로고    scopus 로고
    • An improved map of conserved regulatory sites for saccharomyces cerevisiae
    • MacIsaac,K.D. et al. (2006) An improved map of conserved regulatory sites for saccharomyces cerevisiae. BMC Bioinformatics, 7, 113.
    • (2006) BMC Bioinformatics , vol.7 , pp. 113
    • MacIsaac, K.D.1
  • 24
    • 0037094434 scopus 로고    scopus 로고
    • Magasanik,B. and KaiserC.A. (2002) Nitrogen regulation in saccharomyces cerevisiae. Gene, 290, 1-18.
    • Magasanik,B. and KaiserC.A. (2002) Nitrogen regulation in saccharomyces cerevisiae. Gene, 290, 1-18.
  • 25
    • 34548749776 scopus 로고    scopus 로고
    • Context-sensitive data integration and prediction of biological networks
    • Myers,C.L. and Troyanskaya,O.G. (2007) Context-sensitive data integration and prediction of biological networks. Bioinformatics, 23, 2322-2330.
    • (2007) Bioinformatics , vol.23 , pp. 2322-2330
    • Myers, C.L.1    Troyanskaya, O.G.2
  • 26
    • 33745431808 scopus 로고    scopus 로고
    • Deciphering principles of transcription regulation in eukaryotic genomes
    • Nguyen,D.H. and D'haeseleer,P. (2006) Deciphering principles of transcription regulation in eukaryotic genomes. Mol. Syst. Biol., 2, 2006.0012.
    • (2006) Mol. Syst. Biol , vol.2 , pp. 0012
    • Nguyen, D.H.1    D'haeseleer, P.2
  • 27
    • 0033597939 scopus 로고    scopus 로고
    • Genetic selection of peptide inhibitors of biological pathways
    • Norman,T.C. et al. (1999) Genetic selection of peptide inhibitors of biological pathways. Science, 285, 591-595.
    • (1999) Science , vol.285 , pp. 591-595
    • Norman, T.C.1
  • 28
    • 0028961858 scopus 로고
    • Role of the saccharomyces cerevisiae general regulatory factor cp1 in methionine biosynthetic gene transcription
    • O'Connell,K.F. et al. (1995) Role of the saccharomyces cerevisiae general regulatory factor cp1 in methionine biosynthetic gene transcription. Mol. Cell Biol., 15, 1879-1888.
    • (1995) Mol. Cell Biol , vol.15 , pp. 1879-1888
    • O'Connell, K.F.1
  • 29
    • 0037020260 scopus 로고    scopus 로고
    • Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of saccharomyces cerevisiae
    • Piper,M.D.W et al. (2002) Reproducibility of oligonucleotide microarray transcriptome analyses. An interlaboratory comparison using chemostat cultures of saccharomyces cerevisiae. J. Biol. Chem., 277, 37001-37008.
    • (2002) J. Biol. Chem , vol.277 , pp. 37001-37008
    • Piper, M.D.W.1
  • 30
    • 33845935641 scopus 로고    scopus 로고
    • Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in saccharomyces cerevisiae
    • Regenberg,B. et al. (2006) Growth-rate regulated genes have profound impact on interpretation of transcriptome profiling in saccharomyces cerevisiae. Genome Biol., 7, R107.
    • (2006) Genome Biol , vol.7
    • Regenberg, B.1
  • 31
    • 0034973630 scopus 로고    scopus 로고
    • Sut1p interaction with cyc8p(ssn6p) relieves hypoxic genes from cyc8p-tup1p repression in saccharomyces cerevisiae
    • Regnacq,M. et al. (2001) Sut1p interaction with cyc8p(ssn6p) relieves hypoxic genes from cyc8p-tup1p repression in saccharomyces cerevisiae. Mol. Microbiol., 40, 1085-1096.
    • (2001) Mol. Microbiol , vol.40 , pp. 1085-1096
    • Regnacq, M.1
  • 32
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: Identifying regulatory modules and their condition-specitic regulators from, gene expression data
    • Segal,E. et al. (2003) Module networks: Identifying regulatory modules and their condition-specitic regulators from, gene expression data. Nat. Genet., 34, 166-176.
    • (2003) Nat. Genet , vol.34 , pp. 166-176
    • Segal, E.1
  • 33
    • 0141961625 scopus 로고    scopus 로고
    • Gcn4 negatively regulates expression of genes subjected to nitrogen catabolite repression
    • Sosa,E. et al. (2003) Gcn4 negatively regulates expression of genes subjected to nitrogen catabolite repression. Biochem. Biophys. Res. Commun., 310, 1175-1180.
    • (2003) Biochem. Biophys. Res. Commun , vol.310 , pp. 1175-1180
    • Sosa, E.1
  • 34
    • 12844281816 scopus 로고    scopus 로고
    • Two-dimensional transcriptome analysis in chemostat cultures. combinatorial effects of oxygen availability and macronutrient limitation in saccharomyces cerevisiae
    • Tai,S.L. et al. (2005) Two-dimensional transcriptome analysis in chemostat cultures. combinatorial effects of oxygen availability and macronutrient limitation in saccharomyces cerevisiae. J. Biol. Chem. 280, 437-447.
    • (2005) J. Biol. Chem , vol.280 , pp. 437-447
    • Tai, S.L.1
  • 35
    • 0141905890 scopus 로고    scopus 로고
    • Evaluation of gene expression measurements from commercial microarray platforms
    • Tan,P.K. et al. (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res., 31 5676-5684.
    • (2003) Nucleic Acids Res , vol.31 , pp. 5676-5684
    • Tan, P.K.1
  • 36
    • 0032961329 scopus 로고    scopus 로고
    • Cloning and characterization of three genes (sut1-3) encoding glucose transporters of the yeast pichia stipitis
    • Weierstall,T. et al. (1999) Cloning and characterization of three genes (sut1-3) encoding glucose transporters of the yeast pichia stipitis. Mol. Microbiol., 31, 871-883.
    • (1999) Mol. Microbiol , vol.31 , pp. 871-883
    • Weierstall, T.1
  • 37
    • 0033976586 scopus 로고    scopus 로고
    • Transfac: An integrated system for gene expression regulation
    • Wingender,E. et al. (2000) Transfac: An integrated system for gene expression regulation. Nucleic Acids Res., 28, 316-319.
    • (2000) Nucleic Acids Res , vol.28 , pp. 316-319
    • Wingender, E.1
  • 38
    • 33645977192 scopus 로고    scopus 로고
    • Modeling the combinatorial functions of multiple transcription factors
    • Yeang,C.-H. and Jaakkola,T. (2006) Modeling the combinatorial functions of multiple transcription factors. J. Comput. Biol., 13, 463-480.
    • (2006) J. Comput. Biol , vol.13 , pp. 463-480
    • Yeang, C.-H.1    Jaakkola, T.2
  • 39
    • 33644855121 scopus 로고    scopus 로고
    • Genome-wide prediction and characterization of interactions between transcription factors in saccharomyces cerevisiae
    • Yu,X. et al. (2006) Genome-wide prediction and characterization of interactions between transcription factors in saccharomyces cerevisiae. Nucleic Acids Res., 34, 917-927.
    • (2006) Nucleic Acids Res , vol.34 , pp. 917-927
    • Yu, X.1
  • 40
    • 0026559542 scopus 로고
    • Regulation of gene expression by oxygen in saccharomyces cerevisiae
    • Zitomer,R.S. and Lowry,C.V. (1992) Regulation of gene expression by oxygen in saccharomyces cerevisiae. Microbiol Rev., 56, 1-11.
    • (1992) Microbiol Rev , vol.56 , pp. 1-11
    • Zitomer, R.S.1    Lowry, C.V.2


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