Research article

Gene expression variation between mouse inbred strains

Rolf Turk¹ , Peter AC 't Hoen¹ , Ellen Sterrenburg¹ , Renée X de Menezes² , Emile J de Meijer¹ , Judith M Boer¹ , Gert-Jan B van Ommen¹ and Johan T den Dunnen¹

¹  Center for Human and Clinical Genetics, Leiden University Medical Center, Wassenaarseweg 72, 2333AL Leiden, Nederland

²  Department of Medical Statistics, Leiden University Medical Center, Wassenaarseweg 72, 2333AL Leiden, Nederland

author email corresponding author email

BMC Genomics 2004, 5:57doi:10.1186/1471-2164-5-57

Published:	18 August 2004

Abstract

Background

In this study, we investigated the effect of genetic background on expression profiles. We analysed the transcriptome of mouse hindlimb muscle of five frequently used mouse inbred strains using spotted oligonucleotide microarrays.

Results

Through ANOVA analysis with a false discovery rate of 10%, we show that 1.4% of the analysed genes is significantly differentially expressed between these mouse strains. Differential expression of several of these genes has been confirmed by quantitative RT-PCR. The number of genes affected by genetic background is approximately ten-fold lower than the number of differentially expressed genes caused by a dystrophic genetic defect.

Conclusions

We conclude that evaluation of the effect of background on gene expression profiles in the tissue under study is an effective and sensible approach when comparing expression patterns in animal models with heterogeneous genetic backgrounds. Genes affected by the genetic background can be excluded in subsequent analyses of the disease-related changes in expression profiles. This is often a more effective strategy than backcrossing and inbreeding to obtain isogenic backgrounds.