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EMBO reports 4, 4, 387–393 (2003)
doi:10.1038/sj.embor.embor798
Published online: 1 April 2003
Monitoring global messenger RNA changes in externally controlled microarray experiments
Jeroen van de Peppel1, 3, Patrick Kemmeren1, 3, Harm van Bakel2, Marijana Radonjic1, Dik van Leenen1 & Frank C.P. Holstege1
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1 Genomics Laboratory, Department of Physiological Chemistry, University Medical Centre Utrecht, Postbus 85060, 3508 AB Utrecht, The Netherlands
2 DMG Section Research, Department of Biomedical Genetics, University Medical Centre Utrecht, Lundlaan 6, 3584 EA Utrecht, The Netherlands
3 These authors contributed equally to this work
To whom correspondence should be addressed
Frank C.P. Holstege Tel: +31 30 2538186; Fax: +3130 2539035; f.c.p.holstege@med.uu.nl
Received 4 December 2002; Accepted 21 January 2003; Published online 1 April 2003.
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Abstract
Expression profiling is a universal tool, with a range of applications that benefit from the accurate determination of differential gene expression. To allow normalization using endogenous transcript levels, current microarray analyses assume that relatively few transcripts vary, or that any changes that occur are balanced. When normalization using endogenous genes is carried out, changes in expression levels are calculated relative to the behaviour of most of the transcripts. This does not reflect absolute changes if global shifts in messenger RNA populations occur. Using external RNA controls, we have set up microarray experiments to monitor global changes. The levels of most mRNAs were found to change during yeast stationary phase and human heat shock when external controls were included. Even small global changes had a significant effect on the number of genes reported as being differentially expressed. This suggests that global mRNA changes occur more frequently than is assumed at present, and shows that monitoring such effects may be important for the accurate determination of changes in gene expression.
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