ObjectiveTo analyze the specific genes and key signaling pathways of human papillomavirus (HPV)-positive head and neck squamous cell carcinoma (HNSCC), thus further to screen valuable biomarker for diagnosis and target treatment for HPV-positive HNSCC, which will provide reference for further study of tumor mechanism.MethodsGene chips from HNSCC patients with the information of HPV infection were selected in GEO (Gene Expression Omnibus, GEO) database. Then, the screened DEG cluster were performed for Gene ontology (GO) analysis and signal pathway enrichment analysis. Protein-to-protein interaction (PPI) network was constructed and specific genes were identified, and further protein interaction network visualization was analyzed. Finally, the discrepant expression level of these specific genes in HPV(+) and HPV(-) head and neck squamous carcinoma were validated and the relationship between the specific genes expression and the prognosis of HNSCC patients were explored through searching database.ResultsA total of 556(305 and 251)differential genes were screened out from GSE52088 and GSE39366 respectively. Among 42 common differential genes, 25 genes were up-regulated and 17 genes down-regulated. Four specific genes including IL-6 (interleukin 6), CD44, MMP-1 (matrix metallopeptidase 1) and CXCL1 (CXC motif chemokine ligand 1) were identified by Cytoscape in two rounds. Signal pathway enrichment analysis showed that specific genes were involved in NOD-like receptor signaling pathway, TNF signaling pathway and other major signaling pathways (P < 0.01). The expression discrepancy of specific genes in HPV(+) versus HPV(-) head and neck squamous carcinomas has been validated. The expression of IL-6 and MMP1 were negatively correlated with the survival prognosis of HNSCC (P < 0.01), which was confirmed by the TCGA database and Cbioportal test.Conclusions Different specific genes were found in HPV-positive HNSCC tissues, which were probably involved in different signal pathways regulation and tumorigenesis. IL-6, CD44, MMP1, CXCL1 were the specific genes. MMP1 and CXCL1 were potential biomarkers for diagnosis and prognosis prediction of HPV(+)HNSCC.IL-6, CD44 were correlated with the prognosis of HNSCC, which were expected to be potential targets for HPV(+) HNSCC treatment.