Comprehensive in silico functional specification of mouse retina transcripts.
BACKGROUND
The retina is a well-defined portion of the central nervous system (CNS) that has been used as a model for CNS development and function studies. The full specification of transcripts in an individual tissue or cell type, like retina, can greatly aid the understanding of the control of cell differentiation and cell function. In this study, we have integrated computational bioinformatics and microarray experimental approaches to classify the tissue specificity and developmental distribution of mouse retina transcripts.


RESULTS
We have classified a set of retina-specific genes using sequence-based screening integrated with computational and retina tissue-specific microarray approaches. 33,737 non-redundant sequences were identified as retina transcript clusters (RTCs) from more than 81,000 mouse retina ESTs. We estimate that about 19,000 to 20,000 genes might express in mouse retina from embryonic to adult stages. 39.1% of the RTCs are not covered by 60,770 RIKEN full-length cDNAs. Through comparison with 2 million mouse ESTs, spectra of neural, retinal, late-generated retinal, and photoreceptor -enriched RTCs have been generated. More than 70% of these RTCs have data from biological experiments confirming their tissue-specific expression pattern. The highest-grade retina-enriched pool covered almost all the known genes encoding proteins involved in photo-transduction.


CONCLUSIONS
This study provides a comprehensive mouse retina transcript profile for further gene discovery in retina and suggests that tissue-specific transcripts contribute substantially to the whole transcriptome.
Zhang
Samuel Shao-Min
SS
Department of Pathology, Yale University School of Medicine, 310 Cedar Street, New Haven, CT 06520, USA. shao-min.zhang@yale.edu
Xu
Xuming
X
Li
Jinming
J
Liu
Mu-Gen
MG
Zhao
Hongyu
H
Soares
M Bento
MB
Barnstable
Colin J
CJ
Fu
Xin-Yuan
XY
D000818:Animals; D002490:Central Nervous System / Q000196:embryology; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D018076:DNA, Complementary / Q000378:metabolism; D020224:Expressed Sequence Tags; D005786:Gene Expression Regulation; D018507:Gene Expression Regulation, Developmental; D015723:Gene Library; D008027:Light; D051379:Mice; D008810:Mice, Inbred C57BL; D015233:Models, Statistical; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods; D012333:RNA, Messenger / Q000378:metabolism; D012160:Retina / Q000196:embryology / Q000378:metabolism*; D012984:Software
D018076:DNA, Complementary; D012333:RNA, Messenger