Supervised analysis studies to identify genes differentially expressed. A) Twenty-one genes that best distinguish UC of the renal pelvis and UC of bladder. q-values were obtained by the FDR controlling procedure on the p-values with Wilcoxon rank sum and signed rank tests. B-C) Gene expression profiles of the genes CLCA2 and GABRA, showing significantly overexpression in bUC relative to rUC (potential biomarkers for distinguishing between bUC and rUC). Bars show the median values for each class. D) Normal samples from bladder and renal pelvis, 778 genes identified, see Additional File 4: Supplementary Table S2, and E) normal bladder and combined UC samples (bUC+rUC as a single class), 558 genes. See Additional File 5: Supplementary Table S3. F) Venn diagram of gene lists in A, D, E).