integrated Systems Tool
for Eye gene discovery


The Challenge:
The identification of genes that function in the development of the eye and its associated defects presents a formidable challenge. In the recent past, however, high-throughput genome-level RNA profiling – termed transcriptomics – has become increasingly applicable on small developing tissues due to technologies such as microarrays and RNA sequencing. Their application to investigate specific eye tissues and cell types holds high promise to impact ocular gene discovery. However, high-throughput gene expression profiling has brought with it new challenges, mainly the effective analysis, compilation, access and visualization of these large amounts of data for prioritizing promising candidates for further analysis.

The Potential:
Presently, the eye research community has generated hundreds of microarray datasets on wild-type mouse lenses at various stages and on lens tissue from specific gene-perturbation mouse mutants that exhibit lens defects or cataracts. The enormous potential of this data lies untapped in public databases such as GEO (Gene Expression Omnibus). This is mainly because as currently deposited, the datasets are in the form of minimally processed files, which for being maximally effective need to be individually downloaded and re-analyzed by the end-user. Further, there does not presently exist a resource where individual datasets can be visualized in the comprehensive context of all the available lens expression data.

The Solution:
To address these concerns and to make these largely under- utilized data available to researchers, we analyzed all the lens microarray gene expression datasets that have been generated using standard Affymetrix and Illumina platforms. Further, we have developed a new version of the web- resource tool iSyTE (integrated Systems Tool for Eye gene discovery) that allows effective access and visualization of these analyzed datasets while also facilitating a variety of downstream analyses.

The Impact:
iSyTE enables the user to: (1) prioritize candidate genes relevant to lens development and cataract, (2) get information on cataract/lens defects- associated transcriptome changes, and (3) analyze expression of new candidates and visualize them in the context of previously defined gene expression in wild-type and specific gene-perturbation mouse mutant lenses.