A comparative gene expression profile of the whole eye from human, mouse, and guinea pig.

Purpose: To characterize and compare gene expression patterns of the whole eyeball among human, mouse, and guinea pig based on expressed sequence tags (ESTs).

Methods: Approximately 10,000 clones were sequenced from the 5'-end for each cDNA library made from mRNAs isolated from whole eyeballs of human, mouse, and guinea pig. ESTs were assembled and analyzed based on standard methods.

Results: We acquired 31,464 high-quality ESTs including 9,949 for the human, 11,495 for the mouse, and 10,020 for the guinea pig cDNA libraries, which were clustered into 12,253 unigenes for all three species. After removal of non-mRNA contaminations, we were able to match 96%, 97%, and 63% of the human, mouse, and guinea pig unigenes to sequences in the nonredundant library in GenBank, respectively. The high-abundance and medium-abundance genes in each library correlate with the anatomic structure and physiologic function of the eye in the three species. The large contribution from the lens in the mouse was related to the abundance of crystallin. Differentially expressed genes were observed among three libraries. Some of them appeared species-specific.

Conclusions: According to their gene expression patterns, guinea pig and human eyes are more similar compared to those of the mouse, making the guinea pig a promising animal model for eye research.