Open Access Research article

Comparative gene expression profiling analysis of urothelial carcinoma of the renal pelvis and bladder

Zhongfa Zhang16*, Kyle A Furge2, Ximing J Yang3, Bin T Teh14 and Donna E Hansel5*

Author Affiliations

1 Laboratory of Cancer Genetics, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA

2 Laboratory of Computational Biology, Van Andel Research Institute, 333 Bostwick Avenue NE, Grand Rapids, MI 49503, USA

3 Department of Pathology, Northwestern University, Feinberg School of Medicine, 251 E. Huron, Chicago, Illinois 60611, USA

4 NCCS-VARI Translational Research Laboratory, National Cancer Centre, 11 Hospital Drive, Singapore 169610

5 Pathology and Laboratory Medicine Institute, Glickman Urological and Kidney Institute, Genomic Medicine Institute and Taussig Cancer Institute, Cleveland Clinic, 9500 Euclid Avenue, Cleveland, OH 44195, USA

6 Center for Systems and Computational Biology, The Wistar Institute, Philadelphia, PA 19104, USA

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BMC Medical Genomics 2010, 3:58  doi:10.1186/1755-8794-3-58

Published: 15 December 2010

Additional files

Additional file 1:

Supplementary Figure S1. Box plot of the gene expression intensities of the samples, using intensities of all genes in the database on a logarithmic scale after normalization.

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Additional file 2:

Supplementary Table S1. Lists of genes differentially expressed between C3 and C4 classes identified in Figure 2A-C by SAM method using the default cutoff value 0.05 on the adjusted p-values.

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Additional file 3:

Supplementary Figure S2. Gene expression profiles of CLCA2 (A) and GABRE (B) in normal urothelium, UC, and subtypes of renal cell carcinoma.

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Additional file 4:

Supplementary Table S2. Lists of genes differentially expressed between rNO and bNO identified in Figure 2D by SAM method using cutoff value 0.001 on the adjusted p-values.

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Additional file 5:

Supplementary Table S3. Lists of genes differentially expressed between bNO and UC (bUC and rUC) identified in Figure 2E by SAM method using cutoff value 0.001 on the adjusted p-values.

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