Abstract
Microarrays are promising tools that are increasingly being applied to the study of circadian rhythms. The large and complex datasets they generate, however, mean they require a new approach on how to design experiments, handle datasets, translate results, and derive conclusions. This technology also requires statistical methods for the correct interpretation of data generated by the microarrays. In this chapter, we provide an overview of analytical methods applied to microarray experiments for the identification of genes with circadian expression.
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References
Curran-Everett, D., Taylor, S., and Kafadar, K. (1998) Fundamental concepts in statistics: elucidation and illustration. J. Appl. Physiol. 85, 775–786.
Curran-Everett, D. (2000) Multiple comparisons: philosophies and illustrations. Am. J. Physiol. Regul. Integr. Comp. Physiol. 279, R1–R8.
Ueda, H. R., Chen, W., Adachi, A., et al. (2002) A transcription factor response element for gene expression during circadian night. Nature 418, 534–539.
Ueda, H. R., Matsumoto, A., Kawamura, M., Iino, M., Tanimura, T., and Hashimoto, S. (2002) Genome-wide transcriptional orchestration of circadian rhythms in Drosophila. J. Biol. Chem. 277, 14,048–14,052.
Storch, K. F., Lipan, O., Leykin, I., et al. (2002) Extensive and divergent circadian gene expression in liver and heart. Nature 417, 78–83.
Panda, S., Antoch, M. P., Miller, B. H., et al. (2002) Coordinated transcription of key pathways in the mouse by the circadian clock. Cell 109, 307–320.
Ceriani, M. F., Hogenesch, J. B., Yanovsky, M., Panda, S., Straume, M., and Kay, S. A. (2002) Genome-wide expression analysis in Drosophila reveals genes controlling circadian behavior. J. Neurosci. 22, 9305–9319.
Harmer, S. L., Hogenesch, J. B., Straume, M., et al. (2000) Orchestrated transcription of key pathways in Arabidopsis by the circadian clock. Science 290, 2110–2113.
Claridge-Chang, A., Wijnen, H., Naef, F., Boothroyd, C., Rajewsky, N., and Young, M. W. (2001) Circadian regulation of gene expression systems in the Drosophila head. Neuron 32, 657–671.
Oishi, K., Miyazaki, K., Kadota, K., et al. (2003) Genome-wide expression analysis of mouse liver reveals CLOCK-regulated circadian output genes. J. Biol. Chem. 278, 41,519–41,527.
Grechez-Cassiau, A., Panda, S., Lacoche, S., et al. (2004) The transcriptional repressor STRA13 regulates a subset of peripheral circadian outputs. J. Biol. Chem. 279, 1141–1150.
Salter, M. G., Franklin, K. A., and Whitelam, G. C. (2003) Gating of the rapid shade-avoidance response by the circadian clock in plants. Nature 426, 680–683.
Lin, Y., Han, M., Shimada, B., et al. (2002) Influence of the period-dependent circadian clock on diurnal, circadian, and aperiodic gene expression in Drosophila melanogaster. Proc. Natl. Acad. Sci. USA 99, 9562–9567.
Kita, Y., Shiozawa, M., Jin, W., et al. (2002) Implications of circadian gene expression in kidney, liver and the effects of fasting on pharmacogenomic studies. Pharmacogenetics 12, 55–65.
Humphries, A., Klein, D., Baler, R., and Carter, D. A. (2002) cDNA array analysis of pineal gene expression reveals circadian rhythmicity of the dominant negative helix-loop-helix protein-encoding gene, Id-1. J. Neuroendocrinol. 14, 101–108.
Hirota, T., Okano, T., Kokame, K., Shirotani-Ikejima, H., Miyata, T., and Fukada, Y. (2002) Glucose down-regulates Per1 and Per2 mRNA levels and induces circadian gene expression in cultured Rat-1 fibroblasts. J. Biol. Chem. 277, 44,244–44,251.
Duffield, G. E., Best, J. D., Meurers, B. H., Bittner, A., Loros, J. J., and Dunlap, J. C. (2002) Circadian programs of transcriptional activation, signaling, and protein turnover revealed by microarray analysis of mammalian cells. Curr. Biol. 12, 551–557.
Akhtar, R. A., Reddy, A. B., Maywood, E. S., 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.
Schaffer, R., Landgraf, J., Accerbi, M., Simon, V., Larson, M., and Wisman, E. (2001) Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis. Plant Cell 13, 113–123.
McDonald, M. J., and Rosbash, M. (2001) Microarray analysis and organization of circadian gene expression in Drosophila. Cell 107, 567–578.
Grundschober, C., Delaunay, F., Puhlhofer, A., et al. (2001) Circadian regulation of diverse gene products revealed by mRNA expression profiling of synchronized fibroblasts. J. Biol. Chem. 276, 46,751–46,758.
Nowrousian, M., Duffield, G. E., Loros, J. J., and Dunlap, J. C. (2003) The frequency gene is required for temperature-dependent regulation of many clock-controlled genes in Neurospora crassa. Genetics, 164, 923–933.
Duffield, G. E. (2003) DNA microarray analyses of circadian timing: the genomic basis of biological time. J. Neuroendocrinol. 15, 991–1002.
Etter, P. D., and Ramaswami, M. (2002) The ups and downs of daily life: profiling circadian gene expression in Drosophila. Bioessays 24, 494–498.
Bolstad, B. M., Irizarry, R. A., Astrand, M., and Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185–193.
Quackenbush, J. (2002) Microarray data normalization and transformation. Nat. Genet. 32 Suppl, 496–501.
Liu, G., Loraine, A.E., Shigeta, R., et al. (2003) NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res. 31, 82–86.
Storey, J. D., and Tibshirani, R. (2003) Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 100, 9440–9445.
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Yamada, R., Ueda, H.R. (2007). Microarrays. In: Rosato, E. (eds) Circadian Rhythms. Methods in Molecular Biology™, vol 362. Humana Press. https://doi.org/10.1007/978-1-59745-257-1_17
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DOI: https://doi.org/10.1007/978-1-59745-257-1_17
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