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

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/ 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.

Figure 1

CD immunohistochemistry. Shown is the image data summary for CD138 (SDC1). The top table provides annotation data including the tissue type, distribution of reaction product in the tissue, localization pattern within histologic cell types and an assessment of the level of protein expression for the immunostaining data. The bottom table provides links to the available images for each annotated sample. Available immunostaining images and additional data can be retrieved by clicking on the links.

Figure 2

CD138 immunostaining images. CD138 (SDC1) immunoreactivity of normal human prostate and bladder (immunoreaction product red-brown; pale blue hematoxylin nuclear counterstain). (A) CD138 staining of human bladder urothelium, assay name CD138 03-035A1. (B) CD138 staining of human prostate atrophic glands, basal epithelial cells and nerve sheath cells, assay name CD138 02-007C 5. Original magnification is 200×.

Figure 3

Single gene search. The expression of CD138 (SDC1) among the four sorted prostate cell populations (CD104⁺ basal epithelial, CD26⁺ luminal epithelial, CD31⁺ endothelial and CD31⁺ stromal fibromuscular) in addition to sorted bladder cell populations (CD13^- and CD13⁺ bladder lamina propria) is illustrated. The Affymetrix signal intensity levels are represented by the grey scale. The data can be displayed in full (A), coalesced with respect to biological replicates (B), probesets (C), or both replicate and probeset (D). Present call boxes have no border, Absent calls have a red border, Marginal call is blue (not shown in this example).

Figure 4

Multiple gene search. Shown is the query output for gene names containing SOX (sex determining region Y box) among the four sorted prostate cell populations (CD104⁺ basal epithelial, CD26⁺ luminal epithelial, CD31⁺ endothelial and CD31⁺ stromal fibromuscular) in addition to sorted bladder cell populations (CD13^- and CD13⁺ bladder lamina propria).