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Volumn 7, Issue 11, 2012, Pages

Circadian Phase Has Profound Effects on Differential Expression Analysis

Author keywords

[No Author keywords available]

Indexed keywords

PLANT RNA;

EID: 84869761559     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0049853     Document Type: Article
Times cited : (41)

References (41)
  • 1
    • 66449087281 scopus 로고    scopus 로고
    • The circadian system in higher plants
    • Harmer SL, (2009) The circadian system in higher plants. Annu Rev Plant Biol 60: 357-377.
    • (2009) Annu Rev Plant Biol , vol.60 , pp. 357-377
    • Harmer, S.L.1
  • 2
    • 51749110466 scopus 로고    scopus 로고
    • Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development
    • Covington MF, Maloof JN, Straume M, Kay SA, Harmer SL, (2008) Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol 9: R130.
    • (2008) Genome Biol , vol.9
    • Covington, M.F.1    Maloof, J.N.2    Straume, M.3    Kay, S.A.4    Harmer, S.L.5
  • 3
    • 33646510841 scopus 로고    scopus 로고
    • FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock
    • Edwards KD, Anderson PE, Hall A, Salathia NS, Locke JC, et al. (2006) FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock. Plant Cell 18: 639-650.
    • (2006) Plant Cell , vol.18 , pp. 639-650
    • Edwards, K.D.1    Anderson, P.E.2    Hall, A.3    Salathia, N.S.4    Locke, J.C.5
  • 4
    • 0034671791 scopus 로고    scopus 로고
    • Orchestrated Transcription of Key Pathways in Arabidopsis by the Circadian Clock
    • Harmer SL, Hogenesch JB, Straume M, Chang H-S, Han B, et al. (2000) Orchestrated Transcription of Key Pathways in Arabidopsis by the Circadian Clock. Science 290: 2110-2113.
    • (2000) Science , vol.290 , pp. 2110-2113
    • Harmer, S.L.1    Hogenesch, J.B.2    Straume, M.3    Chang, H.-S.4    Han, B.5
  • 5
    • 0035108613 scopus 로고    scopus 로고
    • Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis
    • Schaffer R, Landgraf J, Accerbi M, Simon V, Larson M, et al. (2001) Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell 13: 113-123.
    • (2001) Plant Cell , vol.13 , pp. 113-123
    • Schaffer, R.1    Landgraf, J.2    Accerbi, M.3    Simon, V.4    Larson, M.5
  • 6
    • 48249105441 scopus 로고    scopus 로고
    • Novel insights from genetic and molecular characterization of the human clock
    • Ptacek LJ, Jones CR, Fu YH, (2007) Novel insights from genetic and molecular characterization of the human clock. Cold Spring Harb Symp Quant Biol 72: 273-277.
    • (2007) Cold Spring Harb Symp Quant Biol , vol.72 , pp. 273-277
    • Ptacek, L.J.1    Jones, C.R.2    Fu, Y.H.3
  • 7
    • 22744451756 scopus 로고    scopus 로고
    • Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage
    • Dodd AN, Salathia N, Hall A, Kevei E, Toth R, et al. (2005) Plant circadian clocks increase photosynthesis, growth, survival, and competitive advantage. Science 309: 630-633.
    • (2005) Science , vol.309 , pp. 630-633
    • Dodd, A.N.1    Salathia, N.2    Hall, A.3    Kevei, E.4    Toth, R.5
  • 9
    • 0032568796 scopus 로고    scopus 로고
    • Constitutive Expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) Gene Disrupts Circadian Rhythms and Suppresses Its Own Expression
    • Wang Z-Y, Tobin EM, (1998) Constitutive Expression of the CIRCADIAN CLOCK ASSOCIATED 1 (CCA1) Gene Disrupts Circadian Rhythms and Suppresses Its Own Expression. Cell 93: 1207-1217.
    • (1998) Cell , vol.93 , pp. 1207-1217
    • Wang, Z.-Y.1    Tobin, E.M.2
  • 10
    • 0006180620 scopus 로고    scopus 로고
    • The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering
    • Schaffer R, Ramsay N, Samach A, Corden S, Putterill J, et al. (1998) The late elongated hypocotyl mutation of Arabidopsis disrupts circadian rhythms and the photoperiodic control of flowering. Cell 93: 1219-1229.
    • (1998) Cell , vol.93 , pp. 1219-1229
    • Schaffer, R.1    Ramsay, N.2    Samach, A.3    Corden, S.4    Putterill, J.5
  • 11
    • 0034604423 scopus 로고    scopus 로고
    • Cloning of the Arabidopsis Clock Gene TOC1, an Autoregulatory Response Regulator Homolog
    • Strayer C, Oyama T, Schultz TF, Raman R, Somers DE, et al. (2000) Cloning of the Arabidopsis Clock Gene TOC1, an Autoregulatory Response Regulator Homolog. Science 289: 768-771.
    • (2000) Science , vol.289 , pp. 768-771
    • Strayer, C.1    Oyama, T.2    Schultz, T.F.3    Raman, R.4    Somers, D.E.5
  • 12
    • 0035800467 scopus 로고    scopus 로고
    • Reciprocal Regulation Between TOC1 and LHY/CCA1 Within the Arabidopsis Circadian Clock
    • Alabadi D, Oyama T, Yanovsky MJ, Harmon FG, Mas P, et al. (2001) Reciprocal Regulation Between TOC1 and LHY/CCA1 Within the Arabidopsis Circadian Clock. Science 293: 880-883.
    • (2001) Science , vol.293 , pp. 880-883
    • Alabadi, D.1    Oyama, T.2    Yanovsky, M.J.3    Harmon, F.G.4    Mas, P.5
  • 13
    • 33644813858 scopus 로고    scopus 로고
    • Positive and Negative Factors Confer Phase-Specific Circadian Regulation of Transcription in Arabidopsis
    • Harmer SL, Kay SA, (2005) Positive and Negative Factors Confer Phase-Specific Circadian Regulation of Transcription in Arabidopsis. Plant Cell 17: 1926-1940.
    • (2005) Plant Cell , vol.17 , pp. 1926-1940
    • Harmer, S.L.1    Kay, S.A.2
  • 14
    • 84859508042 scopus 로고    scopus 로고
    • Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator
    • Huang W, Perez-Garcia P, Pokhilko A, Millar AJ, Antoshechkin I, et al. (2012) Mapping the Core of the Arabidopsis Circadian Clock Defines the Network Structure of the Oscillator. Science.
    • (2012) Science
    • Huang, W.1    Perez-Garcia, P.2    Pokhilko, A.3    Millar, A.J.4    Antoshechkin, I.5
  • 16
    • 77952919484 scopus 로고    scopus 로고
    • PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the Arabidopsis circadian clock
    • Nakamichi N, Kiba T, Henriques R, Mizuno T, Chua NH, et al. (2010) PSEUDO-RESPONSE REGULATORS 9, 7, and 5 are transcriptional repressors in the Arabidopsis circadian clock. Plant Cell 22: 594-605.
    • (2010) Plant Cell , vol.22 , pp. 594-605
    • Nakamichi, N.1    Kiba, T.2    Henriques, R.3    Mizuno, T.4    Chua, N.H.5
  • 17
    • 79953730633 scopus 로고    scopus 로고
    • REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock
    • Rawat R, Takahashi N, Hsu PY, Jones MA, Schwartz J, et al. (2011) REVEILLE8 and PSEUDO-REPONSE REGULATOR5 form a negative feedback loop within the Arabidopsis circadian clock. PLoS Genet 7: e1001350.
    • (2011) PLoS Genet , vol.7
    • Rawat, R.1    Takahashi, N.2    Hsu, P.Y.3    Jones, M.A.4    Schwartz, J.5
  • 18
    • 0035977158 scopus 로고    scopus 로고
    • Microarray analysis and organization of circadian gene expression in Drosophila
    • McDonald MJ, Rosbash M, (2001) Microarray analysis and organization of circadian gene expression in Drosophila. Cell 107: 567-578.
    • (2001) Cell , vol.107 , pp. 567-578
    • McDonald, M.J.1    Rosbash, M.2
  • 19
    • 14644422162 scopus 로고    scopus 로고
    • Global analysis of circadian expression in the cyanobacterium Synechocystis sp. strain PCC 6803
    • Kucho K, Okamoto K, Tsuchiya Y, Nomura S, Nango M, et al. (2005) Global analysis of circadian expression in the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol 187: 2190-2199.
    • (2005) J Bacteriol , vol.187 , pp. 2190-2199
    • Kucho, K.1    Okamoto, K.2    Tsuchiya, Y.3    Nomura, S.4    Nango, M.5
  • 20
    • 0037006795 scopus 로고    scopus 로고
    • Circadian cycling of the mouse liver transcriptome, as revealed by cDNA microarray, is driven by the suprachiasmatic nucleus
    • Akhtar RA, Reddy AB, Maywood ES, Clayton JD, King VM, et al. (2002) Circadian cycling of the mouse liver transcriptome, as revealed by cDNA microarray, is driven by the suprachiasmatic nucleus. Curr Biol 12: 540-550.
    • (2002) Curr Biol , vol.12 , pp. 540-550
    • Akhtar, R.A.1    Reddy, A.B.2    Maywood, E.S.3    Clayton, J.D.4    King, V.M.5
  • 21
    • 18444414586 scopus 로고    scopus 로고
    • Coordinated transcription of key pathways in the mouse by the circadian clock
    • Panda S, Antoch MP, Miller BH, Su AI, Schook AB, et al. (2002) Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109: 307-320.
    • (2002) Cell , vol.109 , pp. 307-320
    • Panda, S.1    Antoch, M.P.2    Miller, B.H.3    Su, A.I.4    Schook, A.B.5
  • 22
    • 34548206704 scopus 로고    scopus 로고
    • The circadian clock regulates auxin signaling and responses in Arabidopsis
    • Covington MF, Harmer SL, (2007) The circadian clock regulates auxin signaling and responses in Arabidopsis. PLoS Biol 5: e222.
    • (2007) PLoS Biol , vol.5
    • Covington, M.F.1    Harmer, S.L.2
  • 23
    • 75949122780 scopus 로고    scopus 로고
    • AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling
    • Rehrauer H, Aquino C, Gruissem W, Henz SR, Hilson P, et al. (2009) AGRONOMICS1: a new resource for Arabidopsis transcriptome profiling. Plant Physiol 152: 487-499.
    • (2009) Plant Physiol , vol.152 , pp. 487-499
    • Rehrauer, H.1    Aquino, C.2    Gruissem, W.3    Henz, S.R.4    Hilson, P.5
  • 24
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical Bayes methods for assessing differential expression in microarray experiments
    • Smyth GK, (2004) Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3.
    • (2004) Stat Appl Genet Mol Biol , vol.3
    • Smyth, G.K.1
  • 25
    • 79955007772 scopus 로고    scopus 로고
    • Functional implication of the MYB transcription factor RVE8/LCL5 in the circadian control of histone acetylation
    • Farinas B, Mas P, (2011) Functional implication of the MYB transcription factor RVE8/LCL5 in the circadian control of histone acetylation. Plant J 66: 318-329.
    • (2011) Plant J , vol.66 , pp. 318-329
    • Farinas, B.1    Mas, P.2
  • 26
    • 1642464802 scopus 로고    scopus 로고
    • DNA microarray time series analysis: automated statistical assessment of circadian rhythms in gene expression patterning
    • Straume M, (2004) DNA microarray time series analysis: automated statistical assessment of circadian rhythms in gene expression patterning. Methods Enzymol 383: 149-166.
    • (2004) Methods Enzymol , vol.383 , pp. 149-166
    • Straume, M.1
  • 27
    • 77957266573 scopus 로고    scopus 로고
    • JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets
    • Hughes ME, Hogenesch JB, Kornacker K, (2010) JTK_CYCLE: an efficient nonparametric algorithm for detecting rhythmic components in genome-scale data sets. J Biol Rhythms 25: 372-380.
    • (2010) J Biol Rhythms , vol.25 , pp. 372-380
    • Hughes, M.E.1    Hogenesch, J.B.2    Kornacker, K.3
  • 29
    • 34247200577 scopus 로고    scopus 로고
    • The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses
    • Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, et al. (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J 50: 347-363.
    • (2007) Plant J , vol.50 , pp. 347-363
    • Kilian, J.1    Whitehead, D.2    Horak, J.3    Wanke, D.4    Weinl, S.5
  • 30
    • 40149105297 scopus 로고    scopus 로고
    • Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules
    • Michael TP, Mockler TC, Breton G, McEntee C, Byer A, et al. (2008) Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PLoS Genet 4: e14.
    • (2008) PLoS Genet , vol.4
    • Michael, T.P.1    Mockler, T.C.2    Breton, G.3    McEntee, C.4    Byer, A.5
  • 31
    • 62349089764 scopus 로고    scopus 로고
    • Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays
    • Hazen SP, Naef F, Quisel T, Gendron JM, Chen H, et al. (2009) Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biol 10: R17.
    • (2009) Genome Biol , vol.10
    • Hazen, S.P.1    Naef, F.2    Quisel, T.3    Gendron, J.M.4    Chen, H.5
  • 33
    • 0035163845 scopus 로고    scopus 로고
    • Transcriptional regulation and function during the human cell cycle
    • Cho RJ, Huang M, Campbell MJ, Dong H, Steinmetz L, et al. (2001) Transcriptional regulation and function during the human cell cycle. Nat Genet 27: 48-54.
    • (2001) Nat Genet , vol.27 , pp. 48-54
    • Cho, R.J.1    Huang, M.2    Campbell, M.J.3    Dong, H.4    Steinmetz, L.5
  • 34
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: open software development for computational biology and bioinformatics
    • Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 5: R80.
    • (2004) Genome Biol , vol.5
    • Gentleman, R.C.1    Carey, V.J.2    Bates, D.M.3    Bolstad, B.4    Dettling, M.5
  • 36
    • 0142121516 scopus 로고    scopus 로고
    • Exploration, normalization, and summaries of high density oligonucleotide array probe level data
    • Irizarry RA, Hobbs B, Collin F, Beazer-Barclay YD, Antonellis KJ, 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    Hobbs, B.2    Collin, F.3    Beazer-Barclay, Y.D.4    Antonellis, K.J.5
  • 40
    • 33846351661 scopus 로고    scopus 로고
    • GIGANTEA acts in blue light signaling and has biochemically separable roles in circadian clock and flowering time regulation
    • Martin-Tryon EL, Kreps JA, Harmer SL, (2007) GIGANTEA acts in blue light signaling and has biochemically separable roles in circadian clock and flowering time regulation. Plant Physiol 143: 473-486.
    • (2007) Plant Physiol , vol.143 , pp. 473-486
    • Martin-Tryon, E.L.1    Kreps, J.A.2    Harmer, S.L.3


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