메뉴 건너뛰기




Volumn 10, Issue 6, 2014, Pages

Cell cycle population effects in perturbation studies

Author keywords

environmental stress response; gene deletion; gene expression; genome wide transcription; growth rate

Indexed keywords

DIAMIDE; DITHIOTHREITOL; HYDROGEN PEROXIDE; MENADIONE; MESSENGER RNA; PHOSPHOPROTEIN PHOSPHATASE; PROTEIN KINASE; TRANSCRIPTION FACTOR; CULTURE MEDIUM;

EID: 84903761634     PISSN: None     EISSN: 17444292     Source Type: Journal    
DOI: 10.15252/msb.20145172     Document Type: Article
Times cited : (89)

References (68)
  • 1
    • 0034730140 scopus 로고    scopus 로고
    • Singular value decomposition for genome-wide expression data processing and modeling
    • Alter O, Brown PO, Botstein D, (2000) Singular value decomposition for genome-wide expression data processing and modeling. Proc Natl Acad Sci USA 97: 10101-10106
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 10101-10106
    • Alter, O.1    Brown, P.O.2    Botstein, D.3
  • 2
    • 0035733887 scopus 로고    scopus 로고
    • Functional genomic analysis of a commercial wine strain of Saccharomyces cerevisiae under differing nitrogen conditions
    • Backhus LE, DeRisi J, Bisson LF, (2001) Functional genomic analysis of a commercial wine strain of Saccharomyces cerevisiae under differing nitrogen conditions. FEMS Yeast Res 1: 111-125
    • (2001) FEMS Yeast Res , vol.1 , pp. 111-125
    • Backhus, L.E.1    Derisi, J.2    Bisson, L.F.3
  • 3
    • 33846798394 scopus 로고    scopus 로고
    • The transcription factor Gcr1 stimulates cell growth by participating in nutrient-responsive gene expression on a global level
    • Barbara KE, Haley TM, Willis KA, Santangelo GM, (2007) The transcription factor Gcr1 stimulates cell growth by participating in nutrient-responsive gene expression on a global level. Mol Genet Genomics 277: 171-188
    • (2007) Mol Genet Genomics , vol.277 , pp. 171-188
    • Barbara, K.E.1    Haley, T.M.2    Willis, K.A.3    Santangelo, G.M.4
  • 4
    • 0035114070 scopus 로고    scopus 로고
    • Osmotic stress causes a G1 cell cycle delay and downregulation of Cln3/Cdc28 activity in Saccharomyces cerevisiae
    • Bellí G, Garí E, Aldea M, Herrero E, (2001) Osmotic stress causes a G1 cell cycle delay and downregulation of Cln3/Cdc28 activity in Saccharomyces cerevisiae. Mol Microbiol 39: 1022-1035
    • (2001) Mol Microbiol , vol.39 , pp. 1022-1035
    • Bellí, G.1    Garí, E.2    Aldea, M.3    Herrero, E.4
  • 6
    • 84861897793 scopus 로고    scopus 로고
    • Mass spectrometry-based proteomics and network biology
    • Bensimon A, Heck AJR, Aebersold R, (2012) Mass spectrometry-based proteomics and network biology. Annu Rev Biochem 81: 379-405
    • (2012) Annu Rev Biochem , vol.81 , pp. 379-405
    • Bensimon, A.1    Heck, A.J.R.2    Aebersold, R.3
  • 7
    • 0034610367 scopus 로고    scopus 로고
    • Genomewide studies of histone deacetylase function in yeast
    • Bernstein BE, Tong JK, Schreiber SL, (2000) Genomewide studies of histone deacetylase function in yeast. Proc Natl Acad Sci USA 97: 13708-13713
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 13708-13713
    • Bernstein, B.E.1    Tong, J.K.2    Schreiber, S.L.3
  • 10
    • 34347387832 scopus 로고    scopus 로고
    • Restriction of DNA replication to the reductive phase of the metabolic cycle protects genome integrity
    • Chen Z, Odstrcil EA, Tu BP, McKnight SL, (2007) Restriction of DNA replication to the reductive phase of the metabolic cycle protects genome integrity. Science 316: 1916-1919
    • (2007) Science , vol.316 , pp. 1916-1919
    • Chen, Z.1    Odstrcil, E.A.2    Tu, B.P.3    McKnight, S.L.4
  • 14
    • 0030669030 scopus 로고    scopus 로고
    • Exploring the metabolic and genetic control of gene expression on a genomic scale
    • DeRisi JL, Iyer VR, Brown PO, (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
  • 16
    • 80051716158 scopus 로고    scopus 로고
    • Commitment to a cellular transition precedes genome-wide transcriptional change
    • Eser U, Falleur-Fettig M, Johnson A, Skotheim JM, (2011) Commitment to a cellular transition precedes genome-wide transcriptional change. Mol Cell 43: 515-527
    • (2011) Mol Cell , vol.43 , pp. 515-527
    • Eser, U.1    Falleur-Fettig, M.2    Johnson, A.3    Skotheim, J.M.4
  • 17
    • 0034817393 scopus 로고    scopus 로고
    • Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression
    • Fazzio TG, Kooperberg C, Goldmark JP, Neal C, Basom R, Delrow J, Tsukiyama T, (2001) Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression. Mol Cell Biol 21: 6450-6460
    • (2001) Mol Cell Biol , vol.21 , pp. 6450-6460
    • Fazzio, T.G.1    Kooperberg, C.2    Goldmark, J.P.3    Neal, C.4    Basom, R.5    Delrow, J.6    Tsukiyama, T.7
  • 18
    • 0033578424 scopus 로고    scopus 로고
    • Systematic changes in gene expression patterns following adaptive evolution in yeast
    • Ferea TL, Botstein D, Brown PO, Rosenzweig RF, (1999) Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci USA 96: 9721-9726
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 9721-9726
    • Ferea, T.L.1    Botstein, D.2    Brown, P.O.3    Rosenzweig, R.F.4
  • 21
    • 0037089082 scopus 로고    scopus 로고
    • Robust G1 checkpoint arrest in budding yeast: Dependence on DNA damage signaling and repair
    • Gerald JNF, Benjamin JM, Kron SJ, (2002) Robust G1 checkpoint arrest in budding yeast: dependence on DNA damage signaling and repair. J Cell Sci 115: 1749-1757
    • (2002) J Cell Sci , vol.115 , pp. 1749-1757
    • Gerald, J.N.F.1    Benjamin, J.M.2    Kron, S.J.3
  • 23
    • 0033592983 scopus 로고    scopus 로고
    • Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins
    • Hardwick JS, Kuruvilla FG, Tong JK, Shamji AF, Schreiber SL, (1999) Rapamycin-modulated transcription defines the subset of nutrient-sensitive signaling pathways directly controlled by the Tor proteins. Proc Natl Acad Sci USA 96: 14866-14870
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 14866-14870
    • Hardwick, J.S.1    Kuruvilla, F.G.2    Tong, J.K.3    Shamji, A.F.4    Schreiber, S.L.5
  • 24
    • 52049084405 scopus 로고    scopus 로고
    • The anchor-away technique: Rapid, conditional establishment of yeast mutant phenotypes
    • Haruki H, Nishikawa J, Laemmli UK, (2008) The anchor-away technique: rapid, conditional establishment of yeast mutant phenotypes. Mol Cell 31: 925-932
    • (2008) Mol Cell , vol.31 , pp. 925-932
    • Haruki, H.1    Nishikawa, J.2    Laemmli, U.K.3
  • 27
    • 34247629588 scopus 로고    scopus 로고
    • Genetic reconstruction of a functional transcriptional regulatory network
    • Hu Z, Killion PJ, Iyer VR, (2007) Genetic reconstruction of a functional transcriptional regulatory network. Nat Genet 39: 683-687
    • (2007) Nat Genet , vol.39 , pp. 683-687
    • Hu, Z.1    Killion, P.J.2    Iyer, V.R.3
  • 31
    • 0033772765 scopus 로고    scopus 로고
    • Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes
    • Jelinsky SA, Estep P, Church GM, Samson LD, (2000) Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Mol Cell Biol 20: 8157-8167
    • (2000) Mol Cell Biol , vol.20 , pp. 8157-8167
    • Jelinsky, S.A.1    Estep, P.2    Church, G.M.3    Samson, L.D.4
  • 32
    • 0018955106 scopus 로고
    • Ribosomal precursor RNA metabolism and cell division in the yeast Saccharomyces cerevisiae
    • Johnston GC, Singer RA, (1980) Ribosomal precursor RNA metabolism and cell division in the yeast Saccharomyces cerevisiae. Mol Genet Genomics 178: 357-360
    • (1980) Mol Genet Genomics , vol.178 , pp. 357-360
    • Johnston, G.C.1    Singer, R.A.2
  • 35
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL, (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25
    • (2009) Genome Biol , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 38
    • 84897397058 scopus 로고    scopus 로고
    • FeatureCounts: An efficient general purpose program for assigning sequence reads to genomic features
    • Liao Y, Smyth GK, Shi W, (2014) featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30: 923-930
    • (2014) Bioinformatics , vol.30 , pp. 923-930
    • Liao, Y.1    Smyth, G.K.2    Shi, W.3
  • 39
    • 47649125318 scopus 로고    scopus 로고
    • Tuning gene expression to changing environments: From rapid responses to evolutionary adaptation
    • Lõpez-Maury L, Marguerat S, Bähler J, (2008) Tuning gene expression to changing environments: from rapid responses to evolutionary adaptation. Nat Rev Genet 9: 583-593
    • (2008) Nat Rev Genet , vol.9 , pp. 583-593
    • Lõpez-Maury, L.1    Marguerat, S.2    Bähler, J.3
  • 40
    • 0042838315 scopus 로고    scopus 로고
    • Expression deconvolution: A reinterpretation of DNA microarray data reveals dynamic changes in cell populations
    • Lu P, Nakorchevskiy A, Marcotte EM, (2003) Expression deconvolution: a reinterpretation of DNA microarray data reveals dynamic changes in cell populations. Proc Natl Acad Sci USA 100: 10370-10375
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 10370-10375
    • Lu, P.1    Nakorchevskiy, A.2    Marcotte, E.M.3
  • 42
    • 0033607161 scopus 로고    scopus 로고
    • Effectors of a developmental mitogen-activated protein kinase cascade revealed by expression signatures of signaling mutants
    • Madhani HD, Galitski T, Lander ES, Fink GR, (1999) Effectors of a developmental mitogen-activated protein kinase cascade revealed by expression signatures of signaling mutants. Proc Natl Acad Sci USA 96: 12530-12535
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 12530-12535
    • Madhani, H.D.1    Galitski, T.2    Lander, E.S.3    Fink, G.R.4
  • 43
    • 0020264211 scopus 로고
    • Quantitative analysis of the heat shock response of Saccharomyces cerevisiae
    • Miller MJ, Xuong NH, Geiduschek EP, (1982) Quantitative analysis of the heat shock response of Saccharomyces 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
  • 45
    • 84859586432 scopus 로고    scopus 로고
    • The response to heat shock and oxidative stress in Saccharomyces cerevisiae
    • Morano KA, Grant CM, Moye-Rowley WS, (2012) The response to heat shock and oxidative stress in Saccharomyces cerevisiae. Genetics 190: 1157-1195
    • (2012) Genetics , vol.190 , pp. 1157-1195
    • Morano, K.A.1    Grant, C.M.2    Moye-Rowley, W.S.3
  • 46
    • 73349085934 scopus 로고    scopus 로고
    • An auxin-based degron system for the rapid depletion of proteins in nonplant cells
    • Nishimura K, Fukagawa T, Takisawa H, Kakimoto T, Kanemaki M, (2009) An auxin-based degron system for the rapid depletion of proteins in nonplant cells. Nat Methods 6: 917-922
    • (2009) Nat Methods , vol.6 , pp. 917-922
    • Nishimura, K.1    Fukagawa, T.2    Takisawa, H.3    Kakimoto, T.4    Kanemaki, M.5
  • 47
    • 0033637520 scopus 로고    scopus 로고
    • New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis
    • Ogawa N, DeRisi J, Brown PO, (2000) New components of a system for phosphate accumulation and polyphosphate metabolism in Saccharomyces cerevisiae revealed by genomic expression analysis. Mol Biol Cell 11: 4309-4321
    • (2000) Mol Biol Cell , vol.11 , pp. 4309-4321
    • Ogawa, N.1    Derisi, J.2    Brown, P.O.3
  • 48
    • 0037721238 scopus 로고    scopus 로고
    • Budding yeast CTDK-I is required for DNA damage-induced transcription
    • Ostapenko D, Solomon MJ, (2003) Budding yeast CTDK-I is required for DNA damage-induced transcription. Eukaryot Cell 2: 274-283
    • (2003) Eukaryot Cell , vol.2 , pp. 274-283
    • Ostapenko, D.1    Solomon, M.J.2
  • 52
    • 75249087100 scopus 로고    scopus 로고
    • EdgeR: A Bioconductor package for differential expression analysis of digital gene expression data
    • Robinson MD, McCarthy DJ, Smyth GK, (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140
    • (2010) Bioinformatics , vol.26 , pp. 139-140
    • Robinson, M.D.1    McCarthy, D.J.2    Smyth, G.K.3
  • 53
    • 0031787969 scopus 로고    scopus 로고
    • Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation
    • Roth FP, Hughes JD, Estep PW, Church GM, (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat Biotechnol 16: 939-945
    • (1998) Nat Biotechnol , vol.16 , pp. 939-945
    • Roth, F.P.1    Hughes, J.D.2    Estep, P.W.3    Church, G.M.4
  • 54
    • 0027509063 scopus 로고
    • Heat shock-mediated cell cycle blockage and G1 cyclin expression in the yeast Saccharomyces cerevisiae
    • Rowley A, Johnston GC, Butler B, Werner-Washburne M, Singer RA, (1993) Heat shock-mediated cell cycle blockage and G1 cyclin expression in the yeast Saccharomyces 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
  • 55
    • 0036628541 scopus 로고    scopus 로고
    • Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization methods
    • Shedden K, Cooper S, (2002) Analysis of cell-cycle gene expression in Saccharomyces cerevisiae using microarrays and multiple synchronization methods. Nucleic Acids Res 30: 2920-2929
    • (2002) Nucleic Acids Res , vol.30 , pp. 2920-2929
    • Shedden, K.1    Cooper, S.2
  • 56
    • 33644872577 scopus 로고    scopus 로고
    • Limma: Linear models for microarray data
    • In, Gentleman R. Carey V. Dudoit S. Irizarry R. Huber W. (eds), pp. New York: Springer
    • Smyth GK, (2005) Limma: linear models for microarray data. In Bioinformatics and Computational Biology Solutions using R and Bioconductor, Gentleman R, Carey V, Dudoit S, Irizarry R, Huber W, (eds), pp 397-420. New York: Springer
    • (2005) Bioinformatics and Computational Biology Solutions Using R and Bioconductor , pp. 397-420
    • Smyth, G.K.1
  • 58
    • 84865249952 scopus 로고    scopus 로고
    • Transcription factors: From enhancer binding to developmental control
    • Spitz F, Furlong EEM, (2012) Transcription factors: from enhancer binding to developmental control. Nat Rev Genet 13: 613-626
    • (2012) Nat Rev Genet , vol.13 , pp. 613-626
    • Spitz, F.1    Furlong, E.E.M.2
  • 59
    • 0034724520 scopus 로고    scopus 로고
    • Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation
    • Travers KJ, Patil CK, Wodicka L, Lockhart DJ, Weissman JS, Walter P, (2000) Functional and genomic analyses reveal an essential coordination between the unfolded protein response and ER-associated degradation. Cell 101: 249-258
    • (2000) Cell , vol.101 , pp. 249-258
    • Travers, K.J.1    Patil, C.K.2    Wodicka, L.3    Lockhart, D.J.4    Weissman, J.S.5    Walter, P.6
  • 60
    • 27944487902 scopus 로고    scopus 로고
    • Logic of the yeast metabolic cycle: Temporal compartmentalization of cellular processes
    • Tu BP, Kudlicki A, Rowicka M, McKnight SL, (2005) Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 310: 1152-1158
    • (2005) Science , vol.310 , pp. 1152-1158
    • Tu, B.P.1    Kudlicki, A.2    Rowicka, M.3    McKnight, S.L.4
  • 63
    • 6344278689 scopus 로고    scopus 로고
    • Characterization of the calcium-mediated response to alkaline stress in Saccharomyces cerevisiae
    • Viladevall L, Serrano R, Ruiz A, Domenech G, Giraldo J, Barcelõ A, Ariño J, (2004) Characterization of the calcium-mediated response to alkaline stress in Saccharomyces cerevisiae. J Biol Chem 279: 43614-43624
    • (2004) J Biol Chem , vol.279 , pp. 43614-43624
    • Viladevall, L.1    Serrano, R.2    Ruiz, A.3    Domenech, G.4    Giraldo, J.5    Barcelõ, A.6    Ariño, J.7
  • 64
    • 0035222942 scopus 로고    scopus 로고
    • Protein interaction maps for model organisms
    • Walhout AJ, Vidal M, (2001) Protein interaction maps for model organisms. Nat Rev Mol Cell Biol 2: 55-62
    • (2001) Nat Rev Mol Cell Biol , vol.2 , pp. 55-62
    • Walhout, A.J.1    Vidal, M.2
  • 66
    • 0038506725 scopus 로고    scopus 로고
    • Multiple pathways are co-regulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8
    • Young ET, Dombek KM, Tachibana C, Ideker T, (2003) Multiple pathways are co-regulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8. J Biol Chem 278: 26146-26158
    • (2003) J Biol Chem , vol.278 , pp. 26146-26158
    • Young, E.T.1    Dombek, K.M.2    Tachibana, C.3    Ideker, T.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.