Prostate gene expression
- Steven G Gray
© BioMed Central Ltd 2001
Received: 15 August 2001
Published: 25 October 2001
The Prostate Expression Database (PEDB) is an on-site database of expressed sequences from both normal and diseased prostate tissues, with an integrated suite of bioinformatics tools for analyzing gene expression.
The Prostate Expression Database (PEDB) is an on-site database of expressed sequences from both normal and diseased prostate tissues, with an integrated suite of bioinformatics tools for analyzing gene expression. Derived from 38 prostate tissue- and cell-type-specific cDNA libraries, the database contains over 77,000 sequences obtained from both full-length cDNAs and expressed sequence tags (ESTs), and represents a broad spectrum of normal and pathological states, including preneoplastic and neoplastic states. Information about the sequences includes tissue source, sequence diversity and transcript abundance.
The site is well laid out with links to different sections, including an overview of the site, a basic search engine, a BLAST engine and the gene expression engine, which allows comparative analyses of both intra- and inter-library data. With the basic search engine, you can do a gene-specific or EST-specific search of the database. The results generated are linked to PubMed, Unigene, and the sequence chromatograms available for each gene or EST. The comparative search engine is limited, in that it only works with Netscape Communicator having Full JDK 1.1 Support. In other words, it is java-based. So if you do not have Netscape Communicator in the right configuration, or only use Internet Explorer, you will not be able to use this function. You need to register (free) to use the site's features.
The attempt to construct molecular fingerprints of the normal, preneoplastic and neoplastic human prostate is the most impressive feature of PEDB.
The transcript abundance (Virtual Expression Analysis) search engine is almost impossible to set up. I tried using Netscape 4.7x (Apple and PC) and Netscape 6.1 (PC) (which runs SDK 2 rather than SDK 1.1), and was unable to get a satisfactory result as the java applet would not initialize. So this site would not be very useful for someone who is not comfortable with computers.