Due to the presence of heterogeneity between these three datasets, we, therefore, adopted the random effects model for the meta-analysis; we found that the expression levels of CDKN2A (log2(fold change) = 1.46, 95%CI: 1.75–2.35), DLAT (log2(fold change) = −0.54, 95%CI: −0.9–−0.15) and FDX1 (log2(fold change) = −1.01, 95%CI: −1.61–−0.42) (Figure 5C–F) were significantly differential between ccRCC and normal tissues, which revealed the role of FDX1 and DLAT as tumor suppressor genes and the role of CDKN2A as a cancer promotor gene. This evidence concerns the gene FDX1 and nonpapillary renal cell carcinoma.