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Microarray analysis of gene expression during the cell cycle.

Cooper S, Shedden K - Cell Chromosome (2003)

Bottom Line: These conclusions are reconsidered using explicit criteria for synchronization and precise criteria for identifying gene expression patterns during the cell cycle.The conclusions regarding cell-cycle-dependent gene expression based on microarray analysis are weakened by arguably problematic choices for synchronization methodology (e.g., whole-culture methods that do not synchronize cells) and questionable statistical rigor for identifying cell-cycle-dependent gene expression.Because of the uncertainties in synchrony methodology, as well as uncertainties in microarray analysis, one should be somewhat skeptical of claims that there are a large number of genes expressed in a cell-cycle-dependent manner.

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Affiliation: Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor Michigan 48109-0620, USA. cooper@umich.edu

ABSTRACT
Microarrays have been applied to the determination of genome-wide expression patterns during the cell cycle of a number of different cells. Both eukaryotic and prokaryotic cells have been studied using whole-culture and selective synchronization methods. The published microarray data on yeast, mammalian, and bacterial cells have been uniformly interpreted as indicating that a large number of genes are expressed in a cell-cycle-dependent manner. These conclusions are reconsidered using explicit criteria for synchronization and precise criteria for identifying gene expression patterns during the cell cycle. The conclusions regarding cell-cycle-dependent gene expression based on microarray analysis are weakened by arguably problematic choices for synchronization methodology (e.g., whole-culture methods that do not synchronize cells) and questionable statistical rigor for identifying cell-cycle-dependent gene expression. Because of the uncertainties in synchrony methodology, as well as uncertainties in microarray analysis, one should be somewhat skeptical of claims that there are a large number of genes expressed in a cell-cycle-dependent manner.

No MeSH data available.


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Illustration of places for application of criteria for synchronization. Numbers refer to criteria in list in Appendix 1 [see additional file 1]. The top box is an activity/cell graph, the lower box is a synchrony curve, and below the synchrony curve are DNA content (left) and size analyses (right) of synchronized cells. Note that the expression of a cycle-dependent gene should peak at the same part of the cell cycle in successive cell cycles. Also, the DNA content should progress as expected through the cell cycle and repeat in the second cycle. The cell size of synchronized cells should have a distribution that is significantly narrower than the unsynchronized, original culture.
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Figure 1: Illustration of places for application of criteria for synchronization. Numbers refer to criteria in list in Appendix 1 [see additional file 1]. The top box is an activity/cell graph, the lower box is a synchrony curve, and below the synchrony curve are DNA content (left) and size analyses (right) of synchronized cells. Note that the expression of a cycle-dependent gene should peak at the same part of the cell cycle in successive cell cycles. Also, the DNA content should progress as expected through the cell cycle and repeat in the second cycle. The cell size of synchronized cells should have a distribution that is significantly narrower than the unsynchronized, original culture.

Mentions: Both the synchrony and microarray aspects of cell-cycle experiments must be considered in order to decide that a particular experiment satisfies rigorous criteria for a well-performed experiment. For synchronized cells (i.e., cells that are cell-cycle-age aligned and are expected to pass through the cell cycle as a unified and coherent cohort) the synchronization method should actually synchronize the cells. Criteria for synchronization are listed in Appendix 1 [additional file 1]. Fig. 1 is a diagrammatic illustration of some of the relevant criteria. Once cells are synchronized, gene expression measurements as the cells pass through the cell cycle should yield reliable data that satisfy rigorous statistical tests (Appendix 2 [additional file 2]).


Microarray analysis of gene expression during the cell cycle.

Cooper S, Shedden K - Cell Chromosome (2003)

Illustration of places for application of criteria for synchronization. Numbers refer to criteria in list in Appendix 1 [see additional file 1]. The top box is an activity/cell graph, the lower box is a synchrony curve, and below the synchrony curve are DNA content (left) and size analyses (right) of synchronized cells. Note that the expression of a cycle-dependent gene should peak at the same part of the cell cycle in successive cell cycles. Also, the DNA content should progress as expected through the cell cycle and repeat in the second cycle. The cell size of synchronized cells should have a distribution that is significantly narrower than the unsynchronized, original culture.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC239863&req=5

Figure 1: Illustration of places for application of criteria for synchronization. Numbers refer to criteria in list in Appendix 1 [see additional file 1]. The top box is an activity/cell graph, the lower box is a synchrony curve, and below the synchrony curve are DNA content (left) and size analyses (right) of synchronized cells. Note that the expression of a cycle-dependent gene should peak at the same part of the cell cycle in successive cell cycles. Also, the DNA content should progress as expected through the cell cycle and repeat in the second cycle. The cell size of synchronized cells should have a distribution that is significantly narrower than the unsynchronized, original culture.
Mentions: Both the synchrony and microarray aspects of cell-cycle experiments must be considered in order to decide that a particular experiment satisfies rigorous criteria for a well-performed experiment. For synchronized cells (i.e., cells that are cell-cycle-age aligned and are expected to pass through the cell cycle as a unified and coherent cohort) the synchronization method should actually synchronize the cells. Criteria for synchronization are listed in Appendix 1 [additional file 1]. Fig. 1 is a diagrammatic illustration of some of the relevant criteria. Once cells are synchronized, gene expression measurements as the cells pass through the cell cycle should yield reliable data that satisfy rigorous statistical tests (Appendix 2 [additional file 2]).

Bottom Line: These conclusions are reconsidered using explicit criteria for synchronization and precise criteria for identifying gene expression patterns during the cell cycle.The conclusions regarding cell-cycle-dependent gene expression based on microarray analysis are weakened by arguably problematic choices for synchronization methodology (e.g., whole-culture methods that do not synchronize cells) and questionable statistical rigor for identifying cell-cycle-dependent gene expression.Because of the uncertainties in synchrony methodology, as well as uncertainties in microarray analysis, one should be somewhat skeptical of claims that there are a large number of genes expressed in a cell-cycle-dependent manner.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor Michigan 48109-0620, USA. cooper@umich.edu

ABSTRACT
Microarrays have been applied to the determination of genome-wide expression patterns during the cell cycle of a number of different cells. Both eukaryotic and prokaryotic cells have been studied using whole-culture and selective synchronization methods. The published microarray data on yeast, mammalian, and bacterial cells have been uniformly interpreted as indicating that a large number of genes are expressed in a cell-cycle-dependent manner. These conclusions are reconsidered using explicit criteria for synchronization and precise criteria for identifying gene expression patterns during the cell cycle. The conclusions regarding cell-cycle-dependent gene expression based on microarray analysis are weakened by arguably problematic choices for synchronization methodology (e.g., whole-culture methods that do not synchronize cells) and questionable statistical rigor for identifying cell-cycle-dependent gene expression. Because of the uncertainties in synchrony methodology, as well as uncertainties in microarray analysis, one should be somewhat skeptical of claims that there are a large number of genes expressed in a cell-cycle-dependent manner.

No MeSH data available.


Related in: MedlinePlus