메뉴 건너뛰기




Volumn 5, Issue , 2004, Pages

Combined analysis of expression data and transcription factor binding sites in the yeast genome

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL DNA; OLIGONUCLEOTIDE; TRANSCRIPTION FACTOR;

EID: 9144248513     PISSN: 14712164     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2164-5-59     Document Type: Article
Times cited : (14)

References (43)
  • 2
    • 0030669030 scopus 로고    scopus 로고
    • Exploring the metabolic and genetic control of gene expression on a genomic scale
    • DeRisi JL, Iyer VR, Brown PO: Exploring the metabolic and genetic control of gene expression on a genomic scale. Science 1997, 278: 680-6.
    • (1997) Science , vol.278 , pp. 680-686
    • DeRisi, J.L.1    Iyer, V.R.2    Brown, P.O.3
  • 4
    • 0001294043 scopus 로고
    • A combinatorial regulatory circuit in budding yeast
    • Edited by: McKnight SL, Yamamoto KR. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press
    • Johnson A: A combinatorial regulatory circuit in budding yeast. In Transcriptional Regulation Edited by: McKnight SL, Yamamoto KR. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 1992:975-1006.
    • (1992) Transcriptional Regulation , pp. 975-1006
    • Johnson, A.1
  • 5
    • 0028325785 scopus 로고
    • Recognition of a DNA operator by a dimer composed of two different homeodomain proteins
    • Goutte C, Johnson AD: Recognition of a DNA operator by a dimer composed of two different homeodomain proteins. EMBO J 1994, 13: 1434-42.
    • (1994) EMBO J. , vol.13 , pp. 1434-1442
    • Goutte, C.1    Johnson, A.D.2
  • 6
    • 0028828745 scopus 로고
    • Crystal structure of the MATa1/MAT α2 homeodomain heterodimer bound to DNA
    • Li T, Stark MR, Johnson AD, Wolberger C: Crystal structure of the MATa1/MAT α2 homeodomain heterodimer bound to DNA. Science 1995, 270: 262-269.
    • (1995) Science , vol.270 , pp. 262-269
    • Li, T.1    Stark, M.R.2    Johnson, A.D.3    Wolberger, C.4
  • 7
    • 0026002757 scopus 로고
    • Crystal structure of a MAT α2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions
    • Wolberger C, Vershon AK, Liu B, Johnson AD, Pabo CO: Crystal structure of a MAT α2 homeodomain-operator complex suggests a general model for homeodomain-DNA interactions. Cell 1991, 67: 517-528.
    • (1991) Cell , vol.67 , pp. 517-528
    • Wolberger, C.1    Vershon, A.K.2    Liu, B.3    Johnson, A.D.4    Pabo, C.O.5
  • 8
    • 0030889410 scopus 로고    scopus 로고
    • The yeast homeodomain protein MATalpha2 shows extended DNA binding specificity in complex with Mcm1
    • Zhong H, Vershon AK: The yeast homeodomain protein MATalpha2 shows extended DNA binding specificity in complex with Mcm1. J Biol Chem 1997, 272: 8402-9.
    • (1997) J. Biol. Chem. , vol.272 , pp. 8402-8409
    • Zhong, H.1    Vershon, A.K.2
  • 9
    • 0032589918 scopus 로고    scopus 로고
    • The yeast a1 and alpha2 homeodomain proteins do not contribute equally to heterodimeric DNA binding
    • Jin Y, Zhong H, Vershon AK: The yeast a1 and alpha2 homeodomain proteins do not contribute equally to heterodimeric DNA binding. Mol Cell Biol 1999, 19: 585-93.
    • (1999) Mol. Cell Biol. , vol.19 , pp. 585-593
    • Jin, Y.1    Zhong, H.2    Vershon, A.K.3
  • 10
    • 0035980146 scopus 로고    scopus 로고
    • Altering the DNA-binding specificity of the yeast matalpha 2 homeodomain protein
    • Mathias JR, Zhong H, Jin Y, Vershon AK: Altering the DNA-binding specificity of the yeast matalpha 2 homeodomain protein. J Biol Chem 2001, 276: 32696-703.
    • (2001) J. Biol. Chem. , vol.276 , pp. 32696-32703
    • Mathias, J.R.1    Zhong, H.2    Jin, Y.3    Vershon, A.K.4
  • 12
    • 0032723678 scopus 로고    scopus 로고
    • Identification of target sites of the alpha2-Mcm1 repressor complex in the yeast genome
    • Zhong H, McCord R, Vershon AK: Identification of target sites of the alpha2-Mcm1 repressor complex in the yeast genome. Genome Res 1999, 9: 1040-7.
    • (1999) Genome Res. , vol.9 , pp. 1040-1047
    • Zhong, H.1    McCord, R.2    Vershon, A.K.3
  • 13
    • 0024165602 scopus 로고
    • Saccharomyces cerevisiae protein involved in plasmid maintenance is necessary for mating of MAT alpha cells
    • Passmore S, Maine GT, Elble R, Christ C, Tye BK: Saccharomyces cerevisiae protein involved in plasmid maintenance is necessary for mating of MAT alpha cells. J Mol Biol 1988, 204: 593-606.
    • (1988) J. Mol. Biol. , vol.204 , pp. 593-606
    • Passmore, S.1    Maine, G.T.2    Elble, R.3    Christ, C.4    Tye, B.K.5
  • 14
    • 0024396954 scopus 로고
    • Yeast repressor alpha 2 binds to its operator cooperatively with yeast protein Mcm1
    • Keleher CA, Passmore S, Johnson AD: Yeast repressor alpha 2 binds to its operator cooperatively with yeast protein Mcm1. Mol Cell Biol 1989, 9: 5228-30.
    • (1989) Mol. Cell Biol. , vol.9 , pp. 5228-5230
    • Keleher, C.A.1    Passmore, S.2    Johnson, A.D.3
  • 15
    • 0023147228 scopus 로고
    • Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters
    • Berg OG, von Hippel PH: Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J Mol Biol 1987, 193: 723-50.
    • (1987) J. Mol. Biol. , vol.193 , pp. 723-750
    • Berg, O.G.1    von Hippel, P.H.2
  • 16
    • 0023894726 scopus 로고
    • Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites
    • Berg OG, von Hippel PH: Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites. J Mol Biol 1988, 200: 709-23.
    • (1988) J. Mol. Biol. , vol.200 , pp. 709-723
    • Berg, O.G.1    von Hippel, P.H.2
  • 17
    • 0021760026 scopus 로고
    • Computer methods to locate signals in nucleic acid sequences
    • Staden R: Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res 1984, 12: 505-19.
    • (1984) Nucleic Acids Res. , vol.12 , pp. 505-519
    • Staden, R.1
  • 18
    • 0032032780 scopus 로고    scopus 로고
    • Specificity, free energy and information content in protein-DNA interactions
    • Stormo GD, Fields DS: Specificity, free energy and information content in protein-DNA interactions. Trends Biochem Sci 1998, 23: 109-13.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 109-113
    • Stormo, G.D.1    Fields, D.S.2
  • 20
    • 1942453302 scopus 로고    scopus 로고
    • Predicting gene expression from sequence
    • Beer MA, Tavazoie S: Predicting gene expression from sequence. Cell 2004, 117: 185-98.
    • (2004) Cell , vol.117 , pp. 185-198
    • Beer, M.A.1    Tavazoie, S.2
  • 21
    • 0037941585 scopus 로고    scopus 로고
    • Module networks: Identifying regulatory modules and their condition-specific regulators from gene expression data
    • Segal E, Shapira M, Regev A, Pe'er D, Botstein D, Koller D, Friedman N: Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet 2003, 34 :166-76.
    • (2003) Nat. Genet. , vol.34 , pp. 166-176
    • Segal, E.1    Shapira, M.2    Regev, A.3    Pe'er, D.4    Botstein, D.5    Koller, D.6    Friedman, N.7
  • 22
    • 2442446708 scopus 로고    scopus 로고
    • Genome-wide discovery of transcriptional modules from DNA sequence and gene expression
    • Segal E, Yelensky R, Koller D: Genome-wide discovery of transcriptional modules from DNA sequence and gene expression. Bioinformatics 2003, 19(Suppl 1): i273-82.
    • (2003) Bioinformatics , vol.19 , Issue.SUPPL. 1
    • Segal, E.1    Yelensky, R.2    Koller, D.3
  • 23
    • 0035135420 scopus 로고    scopus 로고
    • Regulatory element detection using correlation with expression
    • Bussemaker HJ, Li H, Siggia ED: Regulatory element detection using correlation with expression. Nat Genet 2001, 27: 167-71.
    • (2001) Nat. Genet. , vol.27 , pp. 167-171
    • Bussemaker, H.J.1    Li, H.2    Siggia, E.D.3
  • 24
    • 0001134626 scopus 로고
    • Pheromone response and signal transduction during mating process of Saccharomyces cerevisiae
    • Edited by: Broach JR. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press
    • Sprague GF, Thorner JW: Pheromone response and signal transduction during mating process of Saccharomyces cerevisiae. In The Molecular and Cellular Biology of the Yeast Saccharomyces - Gene Expression Edited by: Broach JR. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press; 1992:657-744.
    • (1992) The Molecular and Cellular Biology of the Yeast Saccharomyces - Gene Expression , pp. 657-744
    • Sprague, G.F.1    Thorner, J.W.2
  • 25
    • 0021854593 scopus 로고
    • Identification and comparison of two sequence elements that confer cell-type specific transcription in yeast
    • Miller AM, MacKay VL, Nasmyth KA: Identification and comparison of two sequence elements that confer cell-type specific transcription in yeast. Nature 1985, 314: 598-603.
    • (1985) Nature , vol.314 , pp. 598-603
    • Miller, A.M.1    MacKay, V.L.2    Nasmyth, K.A.3
  • 26
    • 0027759277 scopus 로고
    • Elements of the yeast pheromone response pathway required for filamentous growth of diploids
    • Liu H, Styles CA, Fink GR: Elements of the yeast pheromone response pathway required for filamentous growth of diploids. Science 1993, 262: 1741-4.
    • (1993) Science , vol.262 , pp. 1741-1744
    • Liu, H.1    Styles, C.A.2    Fink, G.R.3
  • 28
    • 0035899933 scopus 로고    scopus 로고
    • Nej1p, a cell type-specific regulator of nonhomologous end joining in yeast
    • Kegel A, Sjostrand JO, Astrom SU: Nej1p, a cell type-specific regulator of nonhomologous end joining in yeast. Curr Biol 2001, 11: 1611-7.
    • (2001) Curr. Biol. , vol.11 , pp. 1611-1617
    • Kegel, A.1    Sjostrand, J.O.2    Astrom, S.U.3
  • 29
    • 0035108094 scopus 로고    scopus 로고
    • Mutations in recombinational repair and in checkpoint control genes suppress the lethal combination of srs2Delta with other DNA repair genes in Saccharomyces cerevisiae
    • Klein HL: Mutations in recombinational repair and in checkpoint control genes suppress the lethal combination of srs2Delta with other DNA repair genes in Saccharomyces cerevisiae. Genetics 2001, 157: 557-65.
    • (2001) Genetics , vol.157 , pp. 557-565
    • Klein, H.L.1
  • 30
    • 0022650212 scopus 로고
    • Activation of meiosis and sporulation by repression of the RME1 product in yeast
    • Mitchell AP, Herskowitz I: Activation of meiosis and sporulation by repression of the RME1 product in yeast. Nature 1986, 319: 738-42.
    • (1986) Nature , vol.319 , pp. 738-742
    • Mitchell, A.P.1    Herskowitz, I.2
  • 31
    • 0024296512 scopus 로고
    • IME1, a positive regulator gene of meiosis in S. cerevisiae
    • Kassir Y, Granot D, Simchen G: IME1, a positive regulator gene of meiosis in S. cerevisiae. Cell 1988, 52: 853-62.
    • (1988) Cell , vol.52 , pp. 853-862
    • Kassir, Y.1    Granot, D.2    Simchen, G.3
  • 32
    • 0026066383 scopus 로고
    • The yeast RME1 gene encodes a putative zinc finger protein that is directly repressed by a1-alpha 2
    • Covitz PA, Herskowitz I, Mitchell AP: The yeast RME1 gene encodes a putative zinc finger protein that is directly repressed by a1-alpha 2. Genes Dev 1991, 5: 1982-9.
    • (1991) Genes Dev. , vol.5 , pp. 1982-1989
    • Covitz, P.A.1    Herskowitz, I.2    Mitchell, A.P.3
  • 33
    • 0032896365 scopus 로고    scopus 로고
    • The PDE1-encoded low-affinity phosphodiesterase in the yeast Saccharomyces cerevisiae has a specific function in controlling agonist-induced cAMP signaling
    • Ma P, Wera S, Van Dijck P, Thevelein JM: The PDE1-encoded low-affinity phosphodiesterase in the yeast Saccharomyces cerevisiae has a specific function in controlling agonist-induced cAMP signaling. Mol Biol Cell 1999, 10: 91-104.
    • (1999) Mol. Biol. Cell , vol.10 , pp. 91-104
    • Ma, P.1    Wera, S.2    Van Dijck, P.3    Thevelein, J.M.4
  • 34
    • 0030979616 scopus 로고    scopus 로고
    • Met31p and Met32p, two related zinc finger proteins, are involved in transcriptional regulation of yeast sulfur amino acid metabolism
    • Blaiseau PL, Isnard AD, Surdin-Kerjan Y, Thomas D: Met31p and Met32p, two related zinc finger proteins, are involved in transcriptional regulation of yeast sulfur amino acid metabolism. Mol Cell Biol 1997, 17: 3640-8.
    • (1997) Mol. Cell Biol. , vol.17 , pp. 3640-3648
    • Blaiseau, P.L.1    Isnard, A.D.2    Surdin-Kerjan, Y.3    Thomas, D.4
  • 36
    • 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 ES: Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature 2003, 423: 241-54.
    • (2003) Nature , vol.423 , pp. 241-254
    • Kellis, M.1    Patterson, N.2    Endrizzi, M.3    Birren, B.4    Lander, E.S.5
  • 38
    • 0026561541 scopus 로고
    • IME4, a gene that mediates MAT and nutritional control of meiosis in Saccharomyces cerevisiae
    • Shah JC, Clancy MJ: IME4, a gene that mediates MAT and nutritional control of meiosis in Saccharomyces cerevisiae. Mol Cell Biol 1992, 12: 1078-86.
    • (1992) Mol. Cell Biol. , vol.12 , pp. 1078-1086
    • Shah, J.C.1    Clancy, M.J.2
  • 39
    • 0036396542 scopus 로고    scopus 로고
    • Rationalization of gene regulation by a eukaryotic transcription factor: Calculation of regulatory region occupancy from predicted binding affinities
    • Liu X, Clarke ND: Rationalization of gene regulation by a eukaryotic transcription factor: calculation of regulatory region occupancy from predicted binding affinities. J Mol Biol 2002, 323: 1-8.
    • (2002) J. Mol. Biol. , vol.323 , pp. 1-8
    • Liu, X.1    Clarke, N.D.2
  • 40
    • 0242574990 scopus 로고    scopus 로고
    • A biophysical approach to transcription factor binding site discovery
    • Djordjevic M, Sengupta AM, Shraiman BI: A biophysical approach to transcription factor binding site discovery. Genome Res 2003, 13: 2381-90.
    • (2003) Genome Res. , vol.13 , pp. 2381-2390
    • Djordjevic, M.1    Sengupta, A.M.2    Shraiman, B.I.3
  • 41
    • 0033388858 scopus 로고    scopus 로고
    • In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment
    • Kuo MH, Allis CD: In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment. Methods 1999, 19: 425-33.
    • (1999) Methods , vol.19 , pp. 425-433
    • Kuo, M.H.1    Allis, C.D.2
  • 42
    • 0036290383 scopus 로고    scopus 로고
    • Engineered improvements in DNA-binding function of the MATa1 homeodomain reveal structural changes involved in combinatorial control
    • Hart B, Mathias JR, Ott D, McNaughton L, Anderson JS, Vershon AK, Baxter SM: Engineered improvements in DNA-binding function of the MATa1 homeodomain reveal structural changes involved in combinatorial control. J Mol Biol 2002, 316: 247-56.
    • (2002) J. Mol. Biol. , vol.316 , pp. 247-256
    • Hart, B.1    Mathias, J.R.2    Ott, D.3    McNaughton, L.4    Anderson, J.S.5    Vershon, A.K.6    Baxter, S.M.7
  • 43
    • 0030950532 scopus 로고    scopus 로고
    • DNA-binding specificity of Mcm1: Operator mutations that alter DNA-bending and transcriptional activities by a MADS box protein
    • Acton TB, Zhong H, Vershon AK: DNA-binding specificity of Mcm1: operator mutations that alter DNA-bending and transcriptional activities by a MADS box protein. Mol Cell Biol 1997, 17: 1881-9.
    • (1997) Mol. Cell Biol. , vol.17 , pp. 1881-1889
    • Acton, T.B.1    Zhong, H.2    Vershon, A.K.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.