As for the subtype-specific altered pathways, there were 25 dysregulated pathways for ccRCC (7 upregulated and 18 downregulated), 11 dysregulated pathways for PRCC (3 upregulated and 8 downregulated), and 12 pathways for ChRCC (7 upregulated and 5 downregulated) (Additional file 3: Table S3). Here, PRCC is linked to nonpapillary renal cell carcinoma.