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E. E. Geisert, L. Lu, R. W. Williams, W. E. Orr, J. P. Templeton, N. E. Freeman-Anderson; Covariance of Gene Expression and Gene Networks in the Mouse Retina. Invest. Ophthalmol. Vis. Sci. 2009;50(13):3996.
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© ARVO (1962-2015); The Authors (2016-present)
Differences in the patterns of gene expressions within the retina account for much of the diversity in ocular phenotype and susceptibility/severity of disease. In studying the structure and diseases of the retina, the laboratory mouse is fast becoming the model of choice. One tool missing in this model system is a systematic database linking differences in gene expression to function and pathophysiology.
In the Mouse Retina Database (MRD), we quantified mRNA levels of the transcriptome from retinas using Illumina Sentrix BeadChip Array MouseWG-6v2 arrays. The Control MRD consists of gene expression data (males and female averages) from BXD recombinant inbred strains and the parental strains (C57Bl/6J and DBA/2J). The web site, GeneNetwork (GN, www.genenetwork.org), presents the MRD to the public, along with probe sequence, SNPs, and complementary phenotypes.
In combination with GN, the MRD provides a large resource for mapping, graphing, analyzing, and testing complex genetic networks. mRNA levels can be used to map quantitative trait loci (QTLs) that contribute to expression differences among the BXD strains, and to establish links between classical ocular phenotypes associated with differences in genomic sequence. This resource can be used to extract unique transcriptome signatures for specific cell types in the retina. We are also able to extract genetic networks that appear to modulate the response of the retina to injury. The MRD complements and extends our previous whole eye transcriptome resource that is in GN (Hamilton Eye Institute Eye Database).
The high level of variation in mRNA levels found among BXD strains of mice can be used to explore and test expression networks underlying variation in retina structure, function, and disease susceptibility. This is the first working draft of the MRD and is available to the public on GeneNetwork (genenetwork.org).
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