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1999 Selected Abstracts from American Urological Association annual meeting

>The Prostate Expression Database:

A Tool for Novel Gene Discovery and the Virtual Analysis of Prostate Gene Expression

Peter S. Nelson, Victoria Hawkins, Camari J. Ferguson, Robert L. Vessella, Paul H. Lange, and Leroy E. Hood. Seattle, WA (Presented by Dr. Nelson)
Introduction :The human genome is estimated to comprise approximately 100,000 genes. In order to confer developmental and functional specificity, only a fraction of this total are active in a given cell type at a given time, and these expressed genes result in the specific phenotype exhibited by the cell. As tumor cells are phenotypically different than their normal counterparts, their set of expressed genes, defined here as the transciptome, differs in a qualitative (different genes expressed) and quantitative fashion. The Prostate Expression Database (PEDB) is a curated relational database and suite of analysis tools designed for the study of prostate gene expression in normal and disease states.
Methods and Results: Expressed Sequence Tags (ESTs) and full-length cDNA sequences derived from more than 40 human prostate cDNA libraries are maintained and represent a wide spectrum of normal and pathological conditions. Detailed library information including tissue source, library construction methods, sequence diversity and abundance are available in a library archive. Prostate ESTs are assembled into distinct species groups using the multiple alignment program CAP2 and are annotated with information from Genbank, dbEST, and the Unigene public sequence databases. Annotated sequences in PEDB are searched using the BLAST algorithm. The differential expression of each EST species can be viewed across all libraries using a Virtual Expression Analysis Tool (VEAT), a graphical user interface written in Java for intra- and inter-library species comparisons. The analysis of PEDB sequences has identified several novel prostate specific genes. Among these are the serine protease Prostase, a prostate-specific androgen-regulated gene.
Summary PEDB provides a resource for investigators studying normal and pathological prostate processes by providing a comprehensive archive of prostate gene expression. We have demonstrated the utility of this database for the discovery and analysis of prostate-specific genes. The PEDB may further be utilized to aid in the construction of non-redundant high-density microarrays and for assembling full-length cDNA sequences. PEDB may be accessed via the World Wide Web at http://www.mbt.washington.edu/PEDB.
Source: 1999 AUA Meeting

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