GSE20347 and GSE38129 were used to validate the different expression levels of hub mRNAs between normal tissues and ESCC tissues with “limma” package in R. The results showed that TBC1D2 and ATP6V0E1 were significantly downregulated in ESCC (log2 FC > 1.5 and FDR < 0.05), while SPI1, RNASE6, C1QB, C1QC, CSF1R, and C1QA are significantly downregulated (log2 FC < −1.5 and FDR < 0.05) (Figure 5). Here, TBC1D2 is linked to esophageal squamous cell carcinoma.