Fig. 1
Gene expression profiles of BBN bladder tumors. a Gene expression in normal bladders (CTRL, gray, n = 6), precancerous bladders from mice exposed to BBN for 4 weeks (BBN PRE, gold, n = 3), and bladders with tumor (BBN TUM, red, n = 5) was assessed by RNA-seq followed by multidimensional scaling analysis. b Heatmap showing expression levels (median-based z-scores) of a list of markers of luminal-, basal-, and p53-like molecular cancer subtypes in bladder samples. c Volcano plots highlighting genes over- (red) and under- (blue) expressed in pre-cancerous (top) or tumoral (bottom) samples compared to control bladders. The number of differentially expressed genes in precancerous bladders and in the BBN tumors is reported. d Scatter plot of gene expression fold changes in the precancerous bladders against controls (y-axis) compared to BBN tumors against controls (x-axis). Point color tracks with the negative logarithm of the bigger false discovery rate (fdr)-adjusted p-value associated with the corresponding gene in the pre-cancerous bladder or in the BBN tumors against controls. Venn diagrams indicate the number of genes consistently up or downregulated. e Heatmap summarizing GO terms enriched in the lists of differentially expressed genes in the pre-cancerous and tumor samples against controls. Color intensity tracks with the negative logarithm of the corresponding p-value (classic Fisher’s exact test)
