Review

Microarray analysis of gene expression during the cell cycle

Stephen Cooper^1* and Kerby Shedden²

• * Corresponding author: Stephen Cooper cooper@umich.edu

Author Affiliations

¹ Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor Michigan 48109-0620, USA

² Department of Statistics, University of Michigan, Ann Arbor Michigan 48109-1092, USA

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Cell & Chromosome 2003, 2:1 doi:10.1186/1475-9268-2-1

Published: 19 September 2003

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.