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Background  Despite papillary renal cell carcinoma (pRCC) being the second most common type of kidney cancer, the underlying molecular mechanism remains unclear. Targeted therapies in the past have not been successful because of the lack of a clear understanding of the molecular mechanism. Hence, exploring the underlying mechanisms and seeking novel biomarkers for pursuing a precise prognostic biomarker and appropriate therapies are critical.    Material and methods  In our research, the differentially expressed genes (DEGs) were screened from the TCGA and GEO databases, and a total of 149 upregulated and 285 downregulated genes were sorted. This was followed by construction of functional enrichment and protein–protein interaction (PPI) network, and then the top 15 DEGs were selected for further analysis. The  P4HB  gene was chosen as our target gene by repetitively validating multiple datasets, and higher levels of  P4HB  expression predicted lower overall survival (OS) in patients with pRCC.    Results  We found that  P4HB  not only connects with immune cell infiltration and co-expression with  PD-1, PD-L2,  and  CTLA-4 , but also has a strong connection with the newly discovered hot gene,  TOX .    Conclusion  We speculate that  P4HB  is a novel gene involved in the progression of pRCC through immunomodulation.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12920-021-01092-w.

Identification of immunization-related new prognostic biomarkers for papillary renal cell carcinoma by integrated bioinformatics analysis