The urologic epithelial stem cell database (UESC) – a web tool for cell type-specific gene expression and immunohistochemistry images of the prostate and bladder
Tóm tắt
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. 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. 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.
Tài liệu tham khảo
Hawkins V, Doll D, Bumgarner R, Smith T, Abajian C, Hood L, Nelson PS: PEDB: the Prostate Expression Database. Nucleic Acids Res. 1999, 27 (1): 204-208. 10.1093/nar/27.1.204.
Li LC, Zhao H, Shiina H, Kane CJ, Dahiya R: PGDB: a curated and integrated database of genes related to the prostate. Nucleic Acids Res. 2003, 31 (1): 291-293. 10.1093/nar/gkg008.
Liu AY, True LD: Characterization of prostate cell types by CD cell surface molecules. Am J Pathol. 2002, 160 (1): 37-43.
Oudes AJ, Campbell DS, Sorensen CM, Walashek LS, True LD, Liu AY: Transcriptomes of human prostate cells. BMC Genomics. 2006, 7: 92-10.1186/1471-2164-7-92.
The Stem Cell Genome Anatomy Project. [http://www.scgap.org/]
Liu AY, Roudier MP, True LD: Heterogeneity in primary and metastatic prostate cancer as defined by cell surface CD profile. Am J Pathol. 2004, 165 (5): 1543-1556.
Pascal LE, Oudes AJ, Petersen TW, Goo YA, Walashek LS, True LD, Liu AY: Molecular and cellular characterization of ABCG2 in the prostate. BMC Urol. 2007, 7 (1): 6-10.1186/1471-2490-7-6.
SCGAP Urologic Epithelial Stem Cells Project. [http://scgap.systemsbiology.net/]
Marzolf B, Deutsch EW, Moss P, Campbell D, Johnson MH, Galitski T: SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology. BMC Bioinformatics. 2006, 7: 286-10.1186/1471-2105-7-286.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T: Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003, 13 (11): 2498-2504. 10.1101/gr.1239303.
Deutsch EW, Ball CA, Berman JJ, Bova GS, Brazma A, Bumgarner RE, Campbell D, Causton HC, Christiansen JH, Daian F, Dauga D, Davidson D, Gimenez G, Goo YA, Grimmond S, Henrich T, Gerrmann BG, Johnson MH, Korb M, Mills JC, Oudes AJ, Parkinson HE, Pascal LE, Pollet N, Quackenbush J, Ramialison M, Ringwald M, Salgado D, Sansone SA, Sherlock G, Christian J Stoeckert J, Swedlow J, Taylor RC, Walashek L, Warford A, Wilkinson DG, Zhou Y, Zon LI, Liu AY, True LD: Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). Nature Biotechnology.
Goo YA, Goodlett DR, Pascal LE, Worthington KD, Vessella RL, True LD, Liu AY: Stromal mesenchyme cell genes of the human prostate and bladder. BMC Urol. 2005, 5: 17-10.1186/1471-2490-5-17.
Oudes AJ, Roach JC, Walashek LS, Eichner LJ, True LD, Vessella RL, Liu AY: Application of Affymetrix array and Massively Parallel Signature Sequencing for identification of genes involved in prostate cancer progression. BMC Cancer. 2005, 5: 86-10.1186/1471-2407-5-86.
The pre-publication history for this paper can be accessed here:http://www.biomedcentral.com/1471-2490/7/19/prepub