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Open Access Highly Accessed Database

The urologic epithelial stem cell database (UESC) – a web tool for cell type-specific gene expression and immunohistochemistry images of the prostate and bladder

Laura E Pascal12*, Eric W Deutsch2, David S Campbell2, Martin Korb2, Lawrence D True3 and Alvin Y Liu12

Author Affiliations

1 Department of Urology, and the Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle WA 98195, USA

2 Institute for Systems Biology, Seattle WA 98103, USA

3 Department of Pathology, University of Washington, Seattle WA 98195, USA

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BMC Urology 2007, 7:19  doi:10.1186/1471-2490-7-19

Published: 11 December 2007

Abstract

Background

Public databases are crucial for analysis of high-dimensional gene and protein expression data. The Urologic Epithelial Stem Cells (UESC) database http://scgap.systemsbiology.net/ webcite is a public database that contains gene and protein information for the major cell types of the prostate, prostate cancer cell lines, and a cancer cell type isolated from a primary tumor. Similarly, such information is available for urinary bladder cell types.

Description

Two major data types were archived in the database, protein abundance localization data from immunohistochemistry images, and transcript abundance data principally from DNA microarray analysis. Data results were organized in modules that were made to operate independently but built upon a core functionality. Gene array data and immunostaining images for human and mouse prostate and bladder were made available for interrogation. Data analysis capabilities include: (1) CD (cluster designation) cell surface protein data. For each cluster designation molecule, a data summary allows easy retrieval of images (at multiple magnifications). (2) Microarray data. Single gene or batch search can be initiated with Affymetrix Probeset ID, Gene Name, or Accession Number together with options of coalescing probesets and/or replicates.

Conclusion

Databases are invaluable for biomedical research, and their utility depends on data quality and user friendliness. UESC provides for database queries and tools to examine cell type-specific gene expression (normal vs. cancer), whereas most other databases contain only whole tissue expression datasets. The UESC database provides a valuable tool in the analysis of differential gene expression in prostate cancer genes in cancer progression.