Fig. 3

Methylation pattern and miRNA expression pattern in PBRM1 mutated ccRCC a Volcano plot of significance of DNA methylation pattern difference (β-difference) between PBRM1 mutated group and “pan-negative” group. Each dot represents one methylation probes. The x axis shows the difference in β-value (β-difference) while the y axis shows the significance by –log transformed p-value obtained from Samr. A probe is called significantly and differentially expressed if its |β-difference| > 0.15 and p-value < 0.01. The red dashed line shows |β-difference| =0.15 or p-value = 0.01. b Heat map of differential expressed methylation probes between PBRM1 mutated group and “pan-negative” group. c Volcano plot of significance of miRNA expression differences between PBRM1 mutated group and “pan-negative” group. Each dot represents one miRNA. The x axis shows log transformed fold changes of miRNA expression while the y axis shows significance by –log₁₀ transformed p-value obtained from edgeR. A probe is called significantly and differentially expressed if its |log(FC)| > 1 and p-value < 0.05. Red dashed line |log(FC)| =1 or p-value = 0.05. d Bar plot of top ten up-regulated miRNAs and down-regulated miRNAs that revealed in PBRM1 mutated samples compared with “pan-negative” ccRCC samples