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Open Access Research article

The Retinome – Defining a reference transcriptome of the adult mammalian retina/retinal pigment epithelium

Heidi L Schulz1, Thomas Goetz12, Juergen Kaschkoetoe1 and Bernhard HF Weber1*

Author affiliations

1 Institute of Human Genetics, Biocenter, University of Wuerzburg, D-97074 Wuerzburg, Germany

2 German Cancer Research Center, Central Spectroscopic Department, D-69120 Heidelberg, Germany

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Citation and License

BMC Genomics 2004, 5:50  doi:10.1186/1471-2164-5-50

Published: 29 July 2004

Abstract

Background

The mammalian retina is a valuable model system to study neuronal biology in health and disease. To obtain insight into intrinsic processes of the retina, great efforts are directed towards the identification and characterization of transcripts with functional relevance to this tissue.

Results

With the goal to assemble a first genome-wide reference transcriptome of the adult mammalian retina, referred to as the retinome, we have extracted 13,037 non-redundant annotated genes from nearly 500,000 published datasets on redundant retina/retinal pigment epithelium (RPE) transcripts. The data were generated from 27 independent studies employing a wide range of molecular and biocomputational approaches. Comparison to known retina-/RPE-specific pathways and established retinal gene networks suggest that the reference retinome may represent up to 90% of the retinal transcripts. We show that the distribution of retinal genes along the chromosomes is not random but exhibits a higher order organization closely following the previously observed clustering of genes with increased expression.

Conclusion

The genome wide retinome map offers a rational basis for selecting suggestive candidate genes for hereditary as well as complex retinal diseases facilitating elaborate studies into normal and pathological pathways. To make this unique resource freely available we have built a database providing a query interface to the reference retinome [1].