True or false: All genes are rhythmic

References

• Lemmer B. Discoveries of rhythms in human biological functions: a historical review. Chronobiol Int. 2009;26:1019–68.
   PubMed Web of Science ®Google Scholar
• Szymanski JS. Die Verteilung von Ruhe und Aktivitätsperioden bei einigen Tierarten. Pfluger Arch ges Physiol. 1918;172: 430–48.
   Google Scholar
• Halberg F. Some physiological and clinical aspects of 24-hour periodicity. J Lancet. 1953;73:20–32.
   PubMedGoogle Scholar
• Konopka RJ, Benzer S. Clock mutants of Drosophila melanogaster. Proc Natl Acad Sci U S A. 1971;68:2112–6.
   PubMed Web of Science ®Google Scholar
• Wager-Smith K, Kay SA. Circadian rhythm genetics: from flies to mice to humans. Nat Genet. 2000;26:23–7.
   PubMed Web of Science ®Google Scholar
• Hardin PE, Hall JC, Rosbash M. Feedback of the Drosophila period gene product on circadian cycling of its messenger RNA levels. Nature. 1990;343(6258):536–40.
   Google Scholar
• Ueda HR, Chen W, Adachi A, Wakamatsu H, Hayashi S, Takasugi T, . A transcription factor response element for gene expression during circadian night. Nature. 2002; 418:534–9.
   PubMed Web of Science ®Google Scholar
• Panda S, Antoch MP, Miller BH, Su AI, Schook AB, Straume M, . Coordinated transcription of key pathways in the mouse by the circadian clock. Cell. 2002;109: 307–20.
   PubMed Web of Science ®Google Scholar
• Duffield GE, Best JD, Meurers BH, Bittner A, Loros JJ, Dunlap JC. Circadian programs of transcriptional activation, signaling, and protein turnover revealed by microarray analysis of mammalian cells. Curr Biol. 2002;12:551–7.
   PubMed Web of Science ®Google Scholar
• Storch KF, Lipan O, Leykin I, Viswanathan N, Davis FC, Wong WH, . Extensive and divergent circadian gene expression in liver and heart. Nature. 2002;417:78–83.
   PubMed Web of Science ®Google Scholar
• Zvonic S, Ptitsyn AA, Kilroy G, Wu X, Conrad SA, Scott LK, . Circadian oscillation of gene expression in murine calvarial bone. J Bone Miner Res. 2007;22:357–65.
   PubMed Web of Science ®Google Scholar
• Zvonic S, Ptitsyn AA, Conrad SA, Scott LK, Floyd ZE, Kilroy G, . Characterization of peripheral circadian clocks in adipose tissues. Diabetes. 2006;55:962–70.
   PubMed Web of Science ®Google Scholar
• Covington MF, Harmer SL. The circadian clock regulates auxin signaling and responses in Arabidopsis. PLoS Biol. 2007;5:e222.
   PubMed Web of Science ®Google Scholar
• Boothroyd CE, Wijnen H, Naef F, Saez L, Young MW. Integration of light and temperature in the regulation of circadian gene expression in Drosophila. PLoS Genet. 2007; 3:e54.
   PubMed Web of Science ®Google Scholar
• Maningat PD, Sen P, Rijnkels M, Sunehag AL, Hadsell DL, Bray M, . Gene expression in the human mammary epithelium during lactation: the milk fat globule transcriptome. Physiol Genomics. 2009;37:12–22.
   PubMed Web of Science ®Google Scholar
• Hogenesch JB, Panda S, Kay S, Takahashi JS. Circadian transcriptional output in the SCN and liver of the mouse. Novartis Found Symp. 2003;253:171–80; discussion 52–5, 102–9, 80–3 passim.
   PubMedGoogle Scholar
• Hughes ME, DiTacchio L, Hayes KR, Vollmers C, Pulivarthy S, Baggs JE, . Harmonics of circadian gene transcription in mammals. PLoS Genet. 2009;5:e1000442.
   PubMed Web of Science ®Google Scholar
• Nelson W, Tong YL, Lee JK, Halberg F. Methods for cosinor-rhythmometry. Chronobiologia. 1979;6:305–23.
   PubMedGoogle Scholar
• Bingham C, Arbogast B, Guillaume GC, Lee JK, Halberg F. Inferential statistical methods for estimating and comparing cosinor parameters. Chronobiologia. 1982;9:397–439.
   PubMedGoogle Scholar
• Harmer SL, Hogenesch JB, Straume M, Chang HS, Han B, Zhu T, . Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science. 2000;290: 2110–3.
   PubMed Web of Science ®Google Scholar
• Ceriani MF, Hogenesch JB, Yanovsky M, Panda S, Straume M, Kay SA. Genome-wide expression analysis in Drosophila reveals genes controlling circadian behavior. J Neurosci. 2002;22:9305–19.
   PubMed Web of Science ®Google Scholar
• Lin Y, Han M, Shimada B, Wang L, Gibler TM, Amarakone A, . Influence of the period-dependent circadian clock on diurnal, circadian, and aperiodic gene expression in Drosophila melanogaster. Proc Natl Acad Sci U S A. 2002; 99:9562–7.
   PubMedGoogle Scholar
• Fisher RA. Tests of significance in harmonic analysis. Proc R Soc Lond A. 1929;125:54–9.
   Google Scholar
• Wichert S, Fokianos K, Strimmer K. Identifying periodically expressed transcripts in microarray time series data. Bioinformatics. 2004;20:5–20.
   PubMed Web of Science ®Google Scholar
• Ahdesmaki M, Lahdesmaki H, Pearson R, Huttunen H, Yli-Harja O. Robust detection of periodic time series measured from biological systems. BMC Bioinformatics. 2005;6: 117.
   Google Scholar
• Ptitsyn AA, Zvonic S, Gimble JM. Permutation test for periodicity in short time series data. BMC Bioinformatics. 2006;7 Suppl 2:S10.
   Google Scholar
• Ptitsyn AA, Zvonic S, Gimble JM. Digital signal processing reveals circadian baseline oscillation in majority of mammalian genes. PLoS Comput Biol. 2007;3:e120.
   Google Scholar
• Doherty CJ, Kay SA. Circadian control of global gene expression patterns. Annu Rev Genet. 2010;44:419–44.
   PubMed Web of Science ®Google Scholar
• Bray MS, Shaw CA, Moore MW, Garcia RA, Zanquetta MM, Durgan DJ, . Disruption of the circadian clock within the cardiomyocyte influences myocardial contractile function, metabolism, and gene expression. Am J Physiol Heart Circ Physiol. 2008;294:H1036–47.
   PubMed Web of Science ®Google Scholar
• McCarthy JJ, Andrews JL, McDearmon EL, Campbell KS, Barber BK, Miller BH, . Identification of the circadian transcriptome in adult mouse skeletal muscle. Physiol Genomics. 2007;31:86–95.
   PubMed Web of Science ®Google Scholar
• McDonald MJ, Rosbash M. Microarray analysis and organization of circadian gene expression in Drosophila. Cell. 2001;107:567–78.
   PubMed Web of Science ®Google Scholar
• Edwards KD, Anderson PE, Hall A, Salathia NS, Locke JC, Lynn JR, . FLOWERING LOCUS C mediates natural variation in the high-temperature response of the Arabidopsis circadian clock. Plant Cell. 2006;18: 639–50.
   PubMed Web of Science ®Google Scholar
• Zambon AC, McDearmon EL, Salomonis N, Vranizan KM, Johansen KL, Adey D, . Time- and exercise-dependent gene regulation in human skeletal muscle. Genome Biol. 2003;4:R61.
   PubMed Web of Science ®Google Scholar
• Covington MF, Maloof JN, Straume M, Kay SA, Harmer SL. Global transcriptome analysis reveals circadian regulation of key pathways in plant growth and development. Genome Biol. 2008;9:R130.
   PubMed Web of Science ®Google Scholar
• Michael TP, Mockler TC, Breton G, McEntee C, Byer A, Trout JD, . Network discovery pipeline elucidates conserved time-of-day-specific cis-regulatory modules. PLoS Genet. 2008;4:e14.
   PubMed Web of Science ®Google Scholar
• Ptitsyn AA, Zvonic S, Conrad SA, Scott LK, Mynatt RL, Gimble JM. Circadian clocks are resounding in peripheral tissues. PLoS Comput Biol. 2006;2(3):e16.
   Google Scholar
• Alan Wee-Chung Liewa N-FL, Xiao-Qin Caoc, Hong Yan. Statistical power of Fisher test for the detection of short periodic gene expression profiles. Pattern Recognition. 2009(42):549–56.
   Google Scholar
• Jan Lindström HK, Esa Ranta. Detecting Periodicity in Short and Noisy Time Series Data. Oikos. 1997;78(2): 406–10.
   Google Scholar
• James H, Horne SLB. A Prescription for Period Analysis of Unevenly Sampled Time Series. The Astrophysical Journal. 1986 March 15(302):757–63.
   Google Scholar
• Klevecz RR, Bolen J, Forrest G, Murray DB. A genomewide oscillation in transcription gates DNA replication and cell cycle. Proc Natl Acad Sci U S A. 2004;101:1200–5.
   PubMed Web of Science ®Google Scholar
• Ptitsyn A. Stochastic resonance reveals ‘pilot light’ expression in mammalian genes. PLoS ONE. 2008;3:e1842.
   Google Scholar
• Selkov E. Stabilization of energy charge, generation of oscillation and multiple steady states in energy metabolism as a result of purely stoichiometric regulation. European Journal of Biochemistry. 1975;59:151–7.
   Google Scholar
• Aon MA, Roussel MR, Cortassa S, O'Rourke B, Murray DB, Beckmann M, . The scale-free dynamics of eukaryotic cells. PLoS One. 2008;3:e3624.
   Google Scholar
• Liu Y, Tsinoremas NF, Johnson CH, Lebedeva NV, Golden SS, Ishiura M, . Circadian orchestration of gene expression in cyanobacteria. Genes Dev. 1995;9: 1469–78.
   PubMed Web of Science ®Google Scholar
• Tu BP, Kudlicki A, Rowicka M, McKnight SL. Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science. 2005;310:1152–8.
   PubMed Web of Science ®Google Scholar
• Murray DB, Beckmann M, Kitano H. Regulation of yeast oscillatory dynamics. Proc Natl Acad Sci U S A. 2007;104: 2241–6.
   PubMed Web of Science ®Google Scholar
• Chen Z, Odstrcil EA, Tu BP, McKnight SL. Restriction of DNA replication to the reductive phase of the metabolic cycle protects genome integrity. Science. 2007;316:1916–9.
   PubMed Web of Science ®Google Scholar
• Klevecz RR, Li CM, Marcus I, Frankel PH. Collective behavior in gene regulation: the cell is an oscillator, the cell cycle a developmental process. FEBS J. 2008;275:2372–84.
   Google Scholar
• Lemberger T, Saladin R, Vazquez M, Assimacopoulos F, Staels B, Desvergne B, . Expression of the peroxisome proliferator-activated receptor alpha gene is stimulated by stress and follows a diurnal rhythm. J Biol Chem. 1996;271:1764–9.
   PubMed Web of Science ®Google Scholar
• Sato TK, Panda S, Miraglia LJ, Reyes TM, Rudic RD, McNamara P, . A functional genomics strategy reveals Rora as a component of the mammalian circadian clock. Neuron. 2004;43:527–37.
   PubMed Web of Science ®Google Scholar
• Stutz AM, Staszkiewicz J, Ptitsyn A, Argyropoulos G. Circadian expression of genes regulating food intake. Obesity (Silver Spring). 2007;15:607–15.
   Web of Science ®Google Scholar
• Refinetti R. Time for sex: nycthemeral distribution of human sexual behavior. J Circadian Rhythms. 2005;3:4.
   PubMedGoogle Scholar
• Ptitsyn AA, Gimble JM. Analysis of circadian pattern reveals tissue-specific alternative transcription in leptin signaling pathway. BMC Bioinformatics. 2007;8 Suppl 7:S15.
   Google Scholar
• Ptitsyn A. Comprehensive analysis of circadian periodic pattern in plant transcriptome. BMC Bioinformatics. 2008; 9 Suppl 9:S18.
   Google Scholar
• Brown EN, Choe Y, Luithardt H, Czeisler CA. A statistical model of the human core-temperature circadian rhythm. Am J Physiol Endocrinol Metab. 2000;279:E669–83.
   PubMed Web of Science ®Google Scholar
• Storch KF, Weitz CJ. Daily rhythms of food-anticipatory behavioral activity do not require the known circadian clock. Proc Natl Acad Sci U S A. 2009;106:6808–13.
   PubMed Web of Science ®Google Scholar