Analysis of cell-cycle-specific gene expression in human cells as determined by microarrays and double-thymidine block synchronization

Proceedings of the National Academy of Sciences of the United States of America
Kerby Shedden, Stephen Cooper

Abstract

Microarray analysis of gene expression patterns for thousands of human genes has led to the proposal that a large number of genes are expressed in a cell-cycle-specific manner. The identification of cyclically expressed genes was based on Affymetrix microarray analysis of gene expression after double-thymidine block synchronization. A statistical reanalysis of the original data leads to three principal findings. (i) Randomized data exhibit periodic patterns of similar or greater strength than the experimental data. This finding suggests that all apparent cyclicities in the expression measurements may arise from chance fluctuations. (ii) The presence of cyclicity and the timing of peak cyclicity in a given gene are not reproduced in two replicate experiments. This fact suggests there is an uncontrolled source of experimental variation that is stronger than the innate variation of gene expression in cells over time. (iii) The amplitude of peak expression in the second cycle is not consistently smaller than the corresponding amplitude in the first cycle. This finding places doubt on the assumption that the cells are actually synchronized. We propose that the microarray results do not support the proposal that there are numerous ce...Continue Reading

References

Dec 7, 1988·Journal of Theoretical Biology·S Cooper
Nov 1, 1987·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·S Cooper
Feb 21, 1982·Journal of Theoretical Biology·S Cooper
Aug 14, 1998·Molecular Cell·R J ChoR W Davis
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Jan 4, 2001·Nature Genetics·R J ChoD J Lockhart
Feb 27, 2001·Journal of Theoretical Biology·S Cooper
May 22, 2001·Cellular and Molecular Life Sciences : CMLS·S Cooper, J A Shayman

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Citations

Aug 15, 2002·Cell Biology International·Stephen Cooper
Jun 5, 2002·Trends in Genetics : TIG·Stephen Cooper
Mar 16, 2011·Chemical Reviews·Morteza MahmoudiSophie Laurent
Feb 24, 2006·Nature Reviews. Cancer·Michael L WhitfieldCharles M Perou
Jul 19, 2012·Nature Reviews. Genetics·Ziv Bar-JosephItamar Simon
Jan 16, 2008·Proceedings of the National Academy of Sciences of the United States of America·Ziv Bar-JosephItamar Simon
Aug 13, 2002·Cloning and Stem Cells·Björn Oback, David Wells
Feb 6, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Gal Chechik, Daphne Koller
May 30, 2009·Molecular Biology of the Cell·Pierre CôteMalcolm Whiteway
Jan 24, 2007·Bioinformatics·Filip Hermans, Elena Tsiporkova
Oct 28, 2003·Cell & Chromosome·Stephen Cooper, Kerby Shedden
Sep 11, 2007·Proceedings of the National Academy of Sciences of the United States of America·Maga RowickaZbyszek Otwinowski
Oct 18, 2014·Molecular and Cellular Biochemistry·Mariana SantosSandra Rebelo
Jan 22, 2015·Proceedings of the National Academy of Sciences of the United States of America·Chung Yu ChanStephen J Benkovic
Oct 5, 2007·Journal of Theoretical Biology·Stephen Cooper, Kerby Shedden
Sep 19, 2008·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Stephen Cooper
Jul 10, 2008·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Meredith E K CalvertLucy F Pemberton
Aug 25, 2015·Nature Methods·Gabriele GutPrisca Liberali
Dec 21, 2002·International Journal of Cancer. Journal International Du Cancer·François BertucciDaniel Birnbaum
Dec 12, 2003·Nature Reviews. Cancer·Peng Liang, Arthur B Pardee
May 4, 2004·Nature Biotechnology·George L Gabor Miklos, Ryszard Maleszka
Aug 10, 2002·The Journal of Biological Chemistry·Margit MengesJames A H Murray
Mar 13, 2003·FASEB Journal : Official Publication of the Federation of American Societies for Experimental Biology·Stephen Cooper

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