NEIBank: EyeBrowse, EyeSAGE and Eye Disease Gene Databases

Abstract

Purpose: : NEIBank (http://neibank.nei.nih.gov) is a project for the creation and organization of genomics resources and bioinformatics tools for vision research.

Methods: : Expressed sequence tag (EST) data for many eye tissues and several species, generated by NEIBank and gathered from public data repositories, are analyzed and displayed using an updated version of GRIST. A new tool allows side by side comparison of EST data for different cDNA libraries from the same or different species. EyeSAGE data for human retina and RPE have been incorporated into NEIBank and eye disease genes and candidate disease gene regions have been compiled from several sources. An eye-centric genome browser, EyeBrowse, based on the UCSC browser, has been developed and incorporates eye expression data for all species with complete genome sequence.

Results: : Web-based analytical and annotation tools in NEIBank allow visualization of gene expression in the eye from raw sequence data to genome alignments. Data can be searched and sorted by chromosome position, tissue, and gene identifiers and functional annotations. Many novel genes, variant transcripts and full length sequences of eye expressed genes have already been identified. Gene expression and eye disease data are integrated through an eye-centric genome browser providing a convenient overview of cDNA and SAGE data from eye combined with known disease genes and candidate disease regions.

Conclusions: : NEIBank, with its annotated, curated databases provides easy access to the repertoire of expressed genes in the eye and to known and candidate eye disease genes.

Keywords: gene/expression • genetics • gene mapping