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Differential gene expression in anatomical compartments of the human eye

Jennifer J Diehn14, Maximilian Diehn2, Michael F Marmor1 and Patrick O Brown23*

Author Affiliations

1 Department of Ophthalmology, Stanford University School of Medicine, Stanford, CA 94305, USA

2 Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA

3 Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA

4 Department of Ophthalmology, University of California, San Francisco, San Francisco, CA 94143, USA

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Genome Biology 2005, 6:R74  doi:10.1186/gb-2005-6-9-r74

Published: 17 August 2005



The human eye is composed of multiple compartments, diverse in form, function, and embryologic origin, that work in concert to provide us with our sense of sight. We set out to systematically characterize the global gene expression patterns that specify the distinctive characteristics of the various eye compartments.


We used DNA microarrays representing approximately 30,000 human genes to analyze gene expression in the cornea, lens, iris, ciliary body, retina, and optic nerve. The distinctive patterns of expression in each compartment could be interpreted in relation to the physiology and cellular composition of each tissue. Notably, the sets of genes selectively expressed in the retina and in the lens were particularly large and diverse. Genes with roles in immune defense, particularly complement components, were expressed at especially high levels in the anterior segment tissues. We also found consistent differences between the gene expression patterns of the macula and peripheral retina, paralleling the differences in cell layer densities between these regions. Based on the hypothesis that genes responsible for diseases that affect a particular eye compartment are likely to be selectively expressed in that compartment, we compared our gene expression signatures with genetic mapping studies to identify candidate genes for diseases affecting the cornea, lens, and retina.


Through genome-scale gene expression profiling, we were able to discover distinct gene expression 'signatures' for each eye compartment and identified candidate disease genes that can serve as a reference database for investigating the physiology and pathophysiology of the eye.