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Journal of Cells

March 2015, Volume 1, 1, pp 1-7

Gene Expression during the Cell Cycle: Obfuscation of Original Cell-Cycle Gene Expression Data by Normalization

Stephen Cooper

Stephen Cooper 1

  1. Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, USA and The Center for Cell Cycle Analysis 1

on Google Scholar
on PubMed

Pages: 1-7

DOI: 10.18488/journal.97/2015.1.1/97.1.1.7

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Abstract:

Normalization of raw data on gene expression during the cell cycle obscures the original experimental data and makes it appear as if all genes have the same numerical level of cyclical expression. Results that would not support gene expression because of minimal variations thus appear, after normalization, to be stronger than they actually are. Consideration of the effect of normalization raises critical questions about many experiments on the cell cycle dependent variation of gene expression—that is, proposed cyclical changes in mRNA content—during the cell cycle. 
Contribution/ Originality
This paper demonstrates that normalization makes minimal variations appear much stronger than they are in the raw data, and thus one should be skeptical of some published results proposing cell-cycle specific gene expression.

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Reference:

  1. Z. Bar-Joseph, Z. Siegfried, M. Brandeis, and B. Brors, "Genome-wide transcriptional analysis of the human cell cycle identifies genes differentially regulated in normal and cancer cells," in Proceedings of the National Academy of Sciences of the United States of America, 2008, pp. 955-960.
  2. L. L. Breeden, "Periodic transcription: A cycle within a cycle," Curr. Biol., vol. 13, pp. 31-38, 2003.
  3. R. J. Cho, M. Huang, M. J. Campbell, and H. Dong, "Transcriptional regulation and function during the human cell cycle," Nature Genetics, vol. 27, pp. 48-54, 2001.
  4. A. Oliva, A. Rosebrock, F. Ferrezuelo, and S. Pyne, "The cell cycle-regulated genes of schizosaccharomyces pombe," PLoS Biol., vol. 3, p. 225, 2005.
  5. D. A. Orlando, C. Y. Lin, A. Bernard, and J. Y. Wang, "Global control of cell-cycle transcription by coupled CDK and network oscillators," Nature, vol. 453, pp. 944-947, 2008.
  6. X. Peng, R. K. Karuturi, L. D. Miller, and K. Lin, "Identification of cell cycle-regulated genes in fission yeast," Molecular Biology of the Cell, vol. 16, pp. 1026-1042, 2005.
  7. G. Rustici, J. Mata, K. Kivinen, and P. Lio, "Periodic gene expression program of the fission yeast cell cycle," Nature Genetics, vol. 36, pp. 809-817, 2004.
  8. P. T. Spellman, G. Sherlock, M. Q. Zhang, and V. R. Lyer, "Comprehensive identification of cell cycle-regulated genes of the yeast saccharomyces cerevisiae by microarray hybridization," Molecular Biology of the Cell, vol. 9, pp. 3273-3297, 1998.
  9. S. Cooper, "A unifying model for the G1 period in prokaryotes and eukaryotes," Nature, vol. 280, pp. 17-19, 1979.
  10. S. Cooper, "Cell cycle analysis and microarrays," Trends in Genetics, vol. 18, pp. 289-290, 2002.
  11. S. Cooper, "On a heuristic point of view concerning the expression of numerous genes during the cell cycle," IUBMB Life, vol. 64, pp. 10-17, 2012.
  12. S. Cooper, "The continuum model and c-myc synthesis during the division cycle," J. Theor. Biol., vol. 135, pp. 393-400, 1988.
  13. S. Cooper, "The continuum model and G1-control of the mammalian cell cycle," Prog Cell Cycle Res., vol. 4, pp. 27-39, 2000.
  14. S. Cooper, "The continuum model: Statistical implications," J. Theor. Biol., vol. 94, pp. 783-800, 1982.
  15. K. Shedden and S. Cooper, "Analysis of cell-cycle-specific gene expression in human cells as determined by microarrays and double-thymidine block synchronization," Proc. Natl. Acad. Sci. USA, vol. 99, pp. 4379-4384, 2002.
  16. K. Shedden and S. Cooper, "Analysis of cell-cycle-specific gene expression in saccharomyces cerevisiae as determined by microarrays and multiple synchronization methods," Nuc. Acids Res., vol. 30, pp. 2920-2929, 2002.
  17. S. Cooper and K. Shedden, "Microarrays and the relationship of mRNA variation to protein variation during the cell cycle," J. Theor. Biol., vol. 249, pp. 574-581, 2007.
  18. S. Cooper, K. Shedden, and D. Vu-Phan, "Invariant mRNA and mitotic protein breakdown solves the Russian doll problem of the cell cycle," Cell Biol. Int., vol. 33, pp. 10-18, 2009.
  19. S. Cooper, "Is whole-culture synchronization biology's perpetual potion pachine?," Trends in Biotechnology, vol. 26, pp. 266-269, 2004.
  20. S. Cooper, "Minimally disturbed, multi-cycle, and reproducible synchrony using a eukaryotic baby machine," Bioessays, vol. 24, pp. 499-501, 2002.
  21. S. Cooper, "Reappraisal of G1-phase arrest and synchronization by lovastatin," Cell Biol. Int., vol. 26, pp. 715-727, 2002.
  22. S. Cooper, "Reappraisal of serum starvation, the restriction point, G0, and G1-phase arrest points," FASEB J., vol. 17, pp. 333-340, 2003.
  23. S. Cooper, "Rejoinder: Whole-culture synchronization cannot, and does not, synchronize cells," Trends in Biotechnology, vol. 22, pp. 274-276, 2004.
  24. S. Cooper, "Rethinking synchronization of mammalian cells for cell-cycle analysis," Cell Mol Life Sci., vol. 6, pp. 1099-1106, 2003.
  25. S. Cooper, "The schaechter-bentzon-maaløe experiment and the analysis of cell cycle events in eukaryotic cells," Trends in Microbiology, vol. 10, pp. 169-173, 2002.
  26. S. Cooper, "Toward a standard system for the mammalian cell cycle," ASM News, vol. 66, pp. 71-75, 2000.
  27. S. Cooper, K. Z. Chen, and S. Ravi, "Thymidine block does not synchronize L1210 mouse leukaemic cells: Implications for cell cycle control, cell cycle analysis and whole-culture synchronization," Cell Prolif., vol. 41, pp. 156-167, 2008.
  28. S. Cooper and M. Gonzalez-Hernandez, "Experimental reconsideration of the utility of serum starvation as a method for synchronizing mammalian cells," Cell Biology International, vol. 33, pp. 71-77, 2009.
  29. S. Cooper, G. Iyer, M. Tarquini, and P. Bissett, "Nocodazole does not synchronize cells: Implications for cell-cycle control and whole-culture synchronization," Cell Tissue Res., vol. 324, pp. 237-242, 2006.
  30. S. Cooper, M. Paulsen, M. Ljungman, and D. Vu-Phan, "Membrane-elution analysis of content of cyclins A, B1, and E during the unperturbed mammalian cell cycle," BMC Cell Division, vol. 2, p. 28, 2007.
  31. S. Cooper, "Schizosaccharomyces pombe grows exponentially during the division cycle with no rate change points," FEMS Yeast Research, vol. 13, pp. 650-658, 2013.

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