Abstract
Recent findings of a genome-wide oscillation involving the transcriptome of the budding yeast Saccharomyces cerevisiae suggest that the most promising path to an understanding of the cell as a dynamic system will proceed from carefully designed time-series sampling followed by the development of signal-processing methods suited to molecular biological datasets. When everything oscillates, conventional biostatistical approaches fall short in identifying functional relationships among genes and their transcripts. Worse, based as they are on steady-state assumptions, such approaches may be misleading. In this chapter, we describe the continuous gated synchrony system and the experiments leading to the concept of genome-wide oscillations, and suggest methods of analysis better suited to dissection of oscillating systems. Using a yeast continuous-culture system, the most precise and stable biological system extant, we explore analytical tools such as wavelet multiresolution decomposition, Fourier analysis, and singular value decomposition to uncover the dynamic architecture of phenotype.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Kauffman, S. and Wille, J. J. (1975) The mitotic oscillator in Physarum polycephalum. J. Theor. Biol. 55, 47–93.
Klevecz, R.R. and Shymko, R. M. (1985) Quasi-exponential generation time distributions from a limit cycle oscillator. Cell Tissue Kinet. 18, 263–271.
Mackey, M. C. and Glass, L. (1977) Oscillation and chaos in physiological control systems. Science 197, 287–289.
Klevecz, R. R. (1998) Phenotypic heterogeneity and genotypic instability in coupled cellular arrays. Physica D 124, 1–10.
Klevecz, R. R., Kros, J., and Gross, S. D. (1978) Phase response versus positive and negative division delay in animal cells. Exp. Cell Res. 116, 285–290.
Klevecz, R. R., Bolen, J., Forrest, G., and Murray, D. B. (2004) A genomewide oscillation in transcription gates DNA replication and cell cycle. Proc. Natl. Acad. Sci. USA 101, 1200–1205.
Klevecz, R. R. and Murray, D. B. (2001) Genome wide oscillations in expression. Mol. Biol. Reports 28, 73–82.
Murray, D. B., Klevecz, R. R., and Lloyd, D. (2003) Generation and maintenance of synchrony in Saccharomyces cerevisiae continuous culture. Exp. Cell. Res. 287, 10–15.
Satroutdinov, A. D., Kuriyama, H., and Kobayashi, H. (1992) Oscillatory metabolism of Saccharomyces cerevisiae in continuous culture. FEMS Microbiol Lett. 77, 261–267.
Murray, D. B., Engelen, F., Lloyd, D., and Kuriyama, H. (1999) Involvement of glutafhione in the regulation of respiratory oscillation during a continuous culture of Saccharomyces cerevisiae. Microbiol. 145, 2739–3747.
Mochan, E. and Pye, E. K. (1973) Respiratory oscillations in adapting yeast cultures. Nat. New Biol. 242, 177–179.
Poole, R. K., and Lloyd, D. Oscillations of enzyme activities during the cell-cycle of a glucose-repressed fission-yeast, Schizosaccharomyces pombe 972h-. Biochem. J. 136, 195–207.
Klevecz, R. R. and Dowse, H. B. (2000) Tuning in the transcriptome: basins of attraction in the yeast cell cycle. Cell Proliferation 33, 209–218.
Klevecz, R. R. (2000) Dynamic architecture of the yeast cell cycle uncovered by wavelet decomposition of expression microarray data. Funct. Integr. Genom. 1, 186–192.
Rifkin, S.A. and Kim, J. (2002) Geometry of gene expression dynamics. Bioinformatics 18, 1176–1183.
Alter, O., Brown, P. O., and Botstein, D. (2000) Singular value decomposition for genome-wide expression data processing and modeling.) Proc. Natl. Acad. Sci. USA 100, 3351–3356.
Alter, O., Brown, P.O., and Botstein, D. (2003) Generalized singular value decomposition for comparative analysis of genome-scale expression datasets of two different organisms. Proc. Natl. Acad. Sci. USA 97, 10,101–10,106.
Warrington, J. A., Nair, A., Mahadevappa, M., and Tsyganskaya, M. (2000) Comparison of human adult and fetal expression and identification of 535 housekee**/maintenance genes. Physiol. Genomics 2, 143–147.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Klevecz, R.R., Li, C.M., Bolen, J.L. (2007). Signal Processing and the Design of Microarray Time-Series Experiments. In: Korenberg, M.J. (eds) Microarray Data Analysis. Methods in Molecular Biology™, vol 377. Humana Press. https://doi.org/10.1007/978-1-59745-390-5_4
Download citation
DOI: https://doi.org/10.1007/978-1-59745-390-5_4
Publisher Name: Humana Press
Print ISBN: 978-1-58829-540-8
Online ISBN: 978-1-59745-390-5
eBook Packages: Springer Protocols