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

Additional files

Additional file 1:

Eigengene significance for mouse strain and brain region. The module eigengene is a single representative expression profile for each sample, based on the first principal component of that module. The first bar plot shows that the Magenta module eigengene is significantly correlated with strain. This indicates that this module is significantly enriched for genes differentially expressed between A/J and C57BL/6J. The second barplot shows that the Red and Pink module eigengenes are significantly correlated with brain region. This indicates that these modules are significantly enriched for genes differentially expressed between amygdala and hippocampus.

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Additional file 2:

Content of the Magenta, Pink, and Red modules. Tables contain probes in Magenta (table 1), Pink (table 2) and Red (table 3) modules. Illumina probe ID, Gene Symbol, Chromosome and expression differences AJ versus C57BL6/J and hippocampus versus amygdala are given. Asterisks in the Probe ID column denote probes containing a known SNP between A/J and C57BL/6J. The last column denotes the cis-regulated genes according to the WTCCC Heterogeneous stock database http://gscan.well.ox.ac.uk/ webcite, with and without known SNPs between included strains. Expression data is transformed (variance stabilizing method) and normalized (robust spline) yielding values comparable to LOG2 values.

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Additional file 3:

Magenta, Pink and Red module membership for all genes. Table contains the correlation between the eigengenes (i.e. 'module membership') for the Red, Pink and Magenta modules with expression values for all 13,627 detected genes on Illumina array.

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Additional file 4:

Network reconstruction on subsets of samples. Networks constructed per strain or per brain region identify distinct modules of co-expressed genes. Dendrograms were produced by average linkage hierarchical clustering of genes using the topological overlap measure. Modules of co-expressed genes were assigned colors corresponding to the branches indicated by the horizontal bar beneath each dendrogram. The color code of the previous module definition (using all samples of both strains) was used to assess preservation. The Red and Pink module are preserved in networks constructed on just A/J (n = 17) or just C57BL/6J samples (n = 18). The Magenta module is found in the networks constructed on just amygdalar (n = 17) or just hippocampus samples (n = 18).

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Additional file 5:

Additional polymorphisms in probe sequences. Sequencing was performed for the probes not containing a known SNP. Probes in the Magenta module showing the highest differential expression between C57BL/6J and A/J were selected. The first and second columns contain the Illumina probe ID and gene symbol of the corresponding target gene. The third column shows the probe sequence for these probes. The forward and reverse primers used are shown in column 4 and 5. The last column indicates whether a SNP (or indel) was found in the probe sequence, which is also indicated in the probe sequence.

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Additional file 6:

Ingenuity Pathway Analysis for the modules of interest. Ingenuity pathway results for genes in the Red (table 1), Pink (table 2) and Magenta (table 3) modules.

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Additional file 7:

Strain * brain tissue interaction effects. A linear model analysis was performed to assess possible interaction effects of brain tissue * strain for all 13627 probes. For this, the R package Limma was used, constructing a linear model with interaction term. Significance was assessed using FDR correction. After this correction, 6 genes showed significant interaction (adjusted p-value < 0.01). The first three columns of the table contain the Illumina Probe ID, Gene Symbol and chromosome. Column four indicates the module in which the probe was grouped using WGCNA analysis. Linear model statistics are given in column five and six.

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