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Open Access Research

Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina

Jindan Yu1, Rafal Farjo1, Sean P MacNee1, Wolfgang Baehr2, Dwight E Stambolian3 and Anand Swaroop14*

Author Affiliations

1 Ophthalmology and Visual Science, University of Michigan, 1000 Wall Street, Ann Arbor, MI 48105, USA

2 Moran Eye Center, University of Utah Health Science Center, Salt Lake City, UT 84132, USA

3 Ophthalmology, University of Pennsylvania School of Medicine, Philadelphia, PA 19014, USA

4 Human Genetics, University of Michigan, 1000 Wall Street, Ann Arbor, MI 48105, USA

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Genome Biology 2003, 4:R65  doi:10.1186/gb-2003-4-10-r65

Published: 22 September 2003

Abstract

Background

As a biomarker of cellular activities, the transcriptome of a specific tissue or cell type during development and disease is of great biomedical interest. We have generated and analyzed 10,000 expressed sequence tags (ESTs) from three mouse eye tissue cDNA libraries: embryonic day 15.5 (M15E) eye, postnatal day 2 (M2PN) eye and adult retina (MRA).

Results

Annotation of 8,633 non-mitochondrial and non-ribosomal high-quality ESTs revealed that 57% of the sequences represent known genes and 43% are unknown or novel ESTs, with M15E having the highest percentage of novel ESTs. Of these, 2,361 ESTs correspond to 747 unique genes and the remaining 6,272 are represented only once. Phototransduction genes are preferentially identified in MRA, whereas transcripts for cell structure and regulatory proteins are highly expressed in the developing eye. Map locations of human orthologs of known genes uncovered a high density of ocular genes on chromosome 17, and identified 277 genes in the critical regions of 37 retinal disease loci. In silico expression profiling identified 210 genes and/or ESTs over-expressed in the eye; of these, more than 26 are known to have vital retinal function. Comparisons between libraries provided a list of temporally regulated genes and/or ESTs. A few of these were validated by qRT-PCR analysis.

Conclusions

Our studies present a large number of potentially interesting genes for biological investigation, and the annotated EST set provides a useful resource for microarray and functional genomic studies.