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Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina
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 (...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2003
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC328454/ https://www.ncbi.nlm.nih.gov/pubmed/14519200 |
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author | Yu, Jindan Farjo, Rafal MacNee, Sean P Baehr, Wolfgang Stambolian, Dwight E Swaroop, Anand |
author_facet | Yu, Jindan Farjo, Rafal MacNee, Sean P Baehr, Wolfgang Stambolian, Dwight E Swaroop, Anand |
author_sort | Yu, Jindan |
collection | PubMed |
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. |
format | Text |
id | pubmed-328454 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2003 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-3284542004-02-05 Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina Yu, Jindan Farjo, Rafal MacNee, Sean P Baehr, Wolfgang Stambolian, Dwight E Swaroop, Anand Genome Biol Research 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. BioMed Central 2003 2003-09-22 /pmc/articles/PMC328454/ /pubmed/14519200 Text en Copyright © 2003 Yu et al.; licensee BioMed Central Ltd. This is an Open Access article: verbatim copying and redistribution of this article are permitted in all media for any purpose, provided this notice is preserved along with the article's original URL. |
spellingShingle | Research Yu, Jindan Farjo, Rafal MacNee, Sean P Baehr, Wolfgang Stambolian, Dwight E Swaroop, Anand Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina |
title | Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina |
title_full | Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina |
title_fullStr | Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina |
title_full_unstemmed | Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina |
title_short | Annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina |
title_sort | annotation and analysis of 10,000 expressed sequence tags from developing mouse eye and adult retina |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC328454/ https://www.ncbi.nlm.nih.gov/pubmed/14519200 |
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