Comprehensive in silico functional specification of mouse retina transcripts

Samuel Shao Min Zhang, Xuming Xu, Jinming Li, Mu Gen Liu, Hongyu Zhao, M. Bento Soares, Colin J. Barnstable, Xin Yuan Fu

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

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. Conclusion: 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.

Original languageEnglish (US)
JournalBMC Genomics
Volume6
DOIs
StatePublished - Mar 18 2005
Externally publishedYes

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Computer Simulation
Retina
Expressed Sequence Tags
Central Nervous System
Organ Specificity
Vertebrate Photoreceptor Cells
Genetic Association Studies
Computational Biology
Transcriptome
Genes
Cell Differentiation
Complementary DNA

ASJC Scopus subject areas

  • Medicine(all)

Cite this

Zhang, S. S. M., Xu, X., Li, J., Liu, M. G., Zhao, H., Soares, M. B., ... Fu, X. Y. (2005). Comprehensive in silico functional specification of mouse retina transcripts. BMC Genomics, 6. https://doi.org/10.1186/1471-2164-6-40

Comprehensive in silico functional specification of mouse retina transcripts. / Zhang, Samuel Shao Min; Xu, Xuming; Li, Jinming; Liu, Mu Gen; Zhao, Hongyu; Soares, M. Bento; Barnstable, Colin J.; Fu, Xin Yuan.

In: BMC Genomics, Vol. 6, 18.03.2005.

Research output: Contribution to journalArticle

Zhang, SSM, Xu, X, Li, J, Liu, MG, Zhao, H, Soares, MB, Barnstable, CJ & Fu, XY 2005, 'Comprehensive in silico functional specification of mouse retina transcripts', BMC Genomics, vol. 6. https://doi.org/10.1186/1471-2164-6-40
Zhang, Samuel Shao Min ; Xu, Xuming ; Li, Jinming ; Liu, Mu Gen ; Zhao, Hongyu ; Soares, M. Bento ; Barnstable, Colin J. ; Fu, Xin Yuan. / Comprehensive in silico functional specification of mouse retina transcripts. In: BMC Genomics. 2005 ; Vol. 6.
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