NEIBank: Est Analysis And Bioinformatics For Ocular Geno

Wistow, Graeme J.

Abstract

The eye is a complex system of highly differentiated tissues of various developmental origins. Many genes essential for eye function are tissue-specific and many of those known are associated with genetic eye diseases. The majority of human expressed genes are known only through expressed sequence tags (ESTs). A project called NEIBank was begun to improve the EST coverage and to develop a molecular encyclopedia for the eye (http://neibank.nei.nih.gov). Many human eye (and also ear) tissues and those of important animal models have now been analyzed. Recent additions include human optic nerve, zebrafish cornea and rhesus monkey and cow lens. The human DNA resource generated by this work has been used to create cDNA microarrays with 13,000 non-redundant human eye expressed sequences and 6500 sequences from mouse eye. A powerful addition to the informatics tools for eye research is EyeBrowse, a dedicated genome browser for eye-expressed genes, produced in collaboration with CIT. http://eyebrowse.cit.nih.gov/genome/; a database for known human eye disease genes and a new tool to compare expression patterns of different tissues and species. In addition, NEIBank now incorporates data from the EyeSAGE project (Duke U) with a custom genome browser track for human eye-derived SAGE data. Another addition is a comprehensive database of human eye disease genes.

Funding Agency

• Agency: National Institute of Health (NIH)
• Institute: National Eye Institute (NEI)
• Type: Intramural Research (Z01)
• Project #: 1Z01EY000320-08
• Application #: 7322284
• Support Year: 8
• Fiscal Year: 2006

Institution

• Name: U.S. National Eye Institute
• Country: United States

Publications

Wistow, Graeme; Peterson, Katherine; Gao, James et al. (2008) NEIBank: genomics and bioinformatics resources for vision research. Mol Vis 14:1327-37

Harding, Rachel L; Howley, Sinead; Baker, Lee J et al. (2008) Lengsin expression and function during zebrafish lens formation. Exp Eye Res 86:807-18

Purkiss, Andrew G; Bateman, Orval A; Wyatt, Keith et al. (2007) Biophysical properties of gammaC-crystallin in human and mouse eye lens: the role of molecular dipoles. J Mol Biol 372:205-22

Popp, Michael P; Liu, Li; Timmers, Adrian et al. (2007) Development of a microarray chip for gene expression in rabbit ocular research. Mol Vis 13:164-73

Wistow, Graeme (2006) The NEIBank project for ocular genomics: data-mining gene expression in human and rodent eye tissues. Prog Retin Eye Res 25:43-77

Wyatt, Keith; White, Helen E; Wang, Luchun et al. (2006) Lengsin is a survivor of an ancient family of class I glutamine synthetases re-engineered by evolution for a role in the vertebrate lens. Structure 14:1823-34

Bowes Rickman, Catherine; Ebright, Jessica N; Zavodni, Zachary J et al. (2006) Defining the human macula transcriptome and candidate retinal disease genes using EyeSAGE. Invest Ophthalmol Vis Sci 47:2305-16

Vihtelic, Thomas S; Fadool, James M; Gao, James et al. (2005) Expressed sequence tag analysis of zebrafish eye tissues for NEIBank. Mol Vis 11:1083-100

Rabinowitz, Yaron S; Dong, Lijin; Wistow, Graeme (2005) Gene expression profile studies of human keratoconus cornea for NEIBank: a novel cornea-expressed gene and the absence of transcripts for aquaporin 5. Invest Ophthalmol Vis Sci 46:1239-46

Ozyildirim, Aylin M; Wistow, Graeme J; Gao, James et al. (2005) The lacrimal gland transcriptome is an unusually rich source of rare and poorly characterized gene transcripts. Invest Ophthalmol Vis Sci 46:1572-80