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Open Access Research article

Gene expression profiling in C57BL/6J and A/J mouse inbred strains reveals gene networks specific for brain regions independent of genetic background

Simone de Jong1, Tova F Fuller2, Esther Janson1, Eric Strengman1, Steve Horvath23, Martien JH Kas4 and Roel A Ophoff125*

Author Affiliations

1 Department of Medical Genetics and Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands

2 Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA

3 Department of Biostatistics, School of Public Health, University of California, Los Angeles, California 90095, USA

4 Department of Neuroscience and Pharmacology, Rudolf Magnus Institute of Neuroscience, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG Utrecht, The Netherlands

5 Center for Neurobehavioral Genetics, University of California, Los Angeles, CA 90095, USA

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BMC Genomics 2010, 11:20  doi:10.1186/1471-2164-11-20

Published: 11 January 2010

Abstract

Background

We performed gene expression profiling of the amygdala and hippocampus taken from inbred mouse strains C57BL/6J and A/J. The selected brain areas are implicated in neurobehavioral traits while these mouse strains are known to differ widely in behavior. Consequently, we hypothesized that comparing gene expression profiles for specific brain regions in these strains might provide insight into the molecular mechanisms of human neuropsychiatric traits. We performed a whole-genome gene expression experiment and applied a systems biology approach using weighted gene co-expression network analysis.

Results

We were able to identify modules of co-expressed genes that distinguish a strain or brain region. Analysis of the networks that are most informative for hippocampus and amygdala revealed enrichment in neurologically, genetically and psychologically related pathways. Close examination of the strain-specific gene expression profiles, however, revealed no functional relevance but a significant enrichment of single nucleotide polymorphisms in the probe sequences used for array hybridization. This artifact was not observed for the modules of co-expressed genes that distinguish amygdala and hippocampus.

Conclusions

The brain-region specific modules were found to be independent of genetic background and are therefore likely to represent biologically relevant molecular networks that can be studied to complement our knowledge about pathways in neuropsychiatric disease.