title: Monitoring global messenger RNA changes in externally controlled microarray experiments.
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.
authors.affiliation: Genomics Laboratory, Department of Physiological Chemistry, University Medical Centre Utrecht, Postbus, Utrecht, The Netherlands.
authors.forename: Jeroen
authors.initials: J
authors.lastname: van de Peppel
authors.forename: Patrick
authors.initials: P
authors.lastname: Kemmeren
authors.forename: Harm
authors.initials: H
authors.lastname: van Bakel
authors.forename: Marijana
authors.initials: M
authors.lastname: Radonjic
authors.forename: Dik
authors.initials: D
authors.lastname: van Leenen
authors.forename: Frank C P
authors.initials: FC
authors.lastname: Holstege
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics; D001943:Breast Neoplasms; D002478:Cells, Cultured; D016895:Culture Media, Serum-Free; D004730:Endothelium, Vascular / Q000502:physiology; D005260:Female; D005786:Gene Expression Regulation; D005798:Genes, Bacterial; D006801:Humans; D008957:Models, Genetic; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D014407:Tumor Cells, Cultured; D014471:Umbilical Veins
chemical_list: D016895:Culture Media, Serum-Free; D012333:RNA, Messenger