Comparative gene expression analysis of murine retina and brain.
OBJECTIVE
Several high-throughput studies have described gene expression in the central nervous system (CNS), and recently there has been increasing interest in analyzing how gene expression compares in different regions of the CNS. As the retina is often used as a model system to study CNS development and function, we compared retina and brain gene expression using microarray analyses.


METHODS
Mouse retina, brain and liver RNA was hybridized to a custom cDNA microarray containing 5,376 genes and ESTs, and the data from the quantified scanned images were analyzed using Bioconductor and SAM. Preferential retina expression was confirmed by real-time PCR. The cellular distribution of genes newly identified as retina enriched genes was determined by immunohistochemistry.


RESULTS
Using stringent statistical analyses we identified 733 genes that were preferentially expressed in retina and 389 in brain. The retina-liver hybridizations identified an additional 837 retina enriched genes. The cellular distribution in the retina was determined for two genes that had not previously been reported to be expressed in the retina, the transcription regulatory proteins EWS and PCPB1. Both proteins were found primarily in the inner nuclear layer. Finally, a comparison of the microarray data to publicly available SAGE and EST library databases demonstrated only limited overlap of the sets of retina enriched genes identified by the different methodologies. The preferential retinal expression of a subset of genes from the microarray, which were not identified as differentially expressed by other methods, was confirmed by quantitative PCR.


CONCLUSIONS
The finding of differences in the groups of identified retina enriched genes from the various profiling techniques supports the use of multiple approaches to obtain a more complete description of retinal gene expression. Characterization of gene expression profiles of retina and brain may facilitate the understanding of the processes that underlie differences between the retina and other parts of the central nervous system.
Hackam
Abigail S
AS
Guerrieri Center for Genetic Engineering and Molecular Ophthalmology at the Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
Qian
Jiang
J
Liu
Dongmei
D
Gunatilaka
Tushara
T
Farkas
Ronald H
RH
Chowers
Itay
I
Kageyama
Masaaki
M
Parmigiani
Giovanni
G
Zack
Donald J
DJ
D000818:Animals; D001921:Brain / Q000378:metabolism*; D020224:Expressed Sequence Tags; D005136:Eye Proteins / Q000235:genetics*; D015870:Gene Expression; D020869:Gene Expression Profiling; D007150:Immunohistochemistry; D008099:Liver / Q000378:metabolism; D051379:Mice; D009419:Nerve Tissue Proteins / Q000235:genetics*; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D012313:RNA / Q000235:genetics; D012160:Retina / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction
D005136:Eye Proteins; D009419:Nerve Tissue Proteins; D012313:RNA