The prostate expression database (PEDB): status and enhancements in 2000 - PubMed (original) (raw)

The prostate expression database (PEDB): status and enhancements in 2000

P S Nelson et al. Nucleic Acids Res. 2000.

Abstract

The Prostate Expression Database (PEDB) is an online resource designed to access and analyze gene expression information derived from the human prostate. PEDB archives >55 000 expressed sequence tags (ESTs) from 43 cDNA libraries in a curated relational database that provides detailed library information including tissue source, library construction methods, sequence diversity and sequence abundance. 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. Recent enhancements to PEDB include: (i) the functional categorization of annotated EST assemblies using a classification scheme developed at The Institute for Genome Research; (ii) catalogs of expressed genes in specific prostate tissue sources designated as transcriptomes; and (iii) the addition of prostate proteome information derived from two-dimensional electrophoreses and mass spectrometry of prostate cancer cell lines. PEDB may be accessed via the WWW at http://www.mbt.washington.edu/PEDB/

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Figures

Figure 1

Results of PEDB cluster annotations against the GenBank, Unigene and dbEST nucleotide sequence database. Joining clusters based upon an identical public database sequence annotation reduced the number of distinct species from 21 114 to 15 953. As the Unigene database is comprised of sequences from both GenBank and dbEST, many PEDB clusters share annotations with two databases. Unannotated PEDB sequences represent clusters that do not have significant homology to any public database sequence.

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