Annotation and analysis of 10,000 expressed sequence tags from 3 mouse eye cDNA libraries

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Publication Type Journal Article
School or College School of Medicine
Department Ophthalmology
Creator Baehr, Wolfgang
Other Author Yu, Jindan; Farjo, Rafal; MacNee, Sean P.; Stambolian, Dwight E.; Swaroop, Anand
Title Annotation and analysis of 10,000 expressed sequence tags from 3 mouse eye cDNA libraries
Date 2003
Description 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.
Type Text
Publisher BioMed Central
Volume 4
Issue 10
Subject Cluster Analysis; DNA, Complementary; Gene Expression Profiling
Subject MESH Aging; Eye; Expressed Sequence Tags
Language eng
Bibliographic Citation Yu J, Farjo R, MacNee SP, Baehr W, Stambolian DE, Swaroop A. (2003). Annotation and analysis of 10,000 Expressed Sequence Tags from 3 mouse eye cDNA libraries. Genome Biol, 4(10), R65
Rights Management (c) [Author(s)]. Creative Commons Attribution License
Format Medium application/pdf
Identifier ir-main,1730
ARK ark:/87278/s6p56623
Setname ir_uspace
Date Created 2012-06-13
Date Modified 2021-05-06
ID 706559
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