Of these, 13 lncRNAs (LINC00460, AL136987.1, MYOSLID, MIR9-3HG, AC073130.1, AC079160.1, LINC01305, AP002478.1, LINC02434, HOTTIP, ATP6V1B1-AS1, AC023310.4, and AL158209.1), eight miRNAs (hsa-miR-411, hsa-miR-4510, hsa-miR-410, hsa-miR-99a, hsa-miR-499a, hsa-miR-4652, hsa-miR-206 and hsa-miR-520e), and 17 mRNAs (CELSR3, STC2, ADGRD2, ZNF541, GRB14, NOSTRIN, TIMP4, HOXB9, ADPRHL1, SPINK1, PTX3, FRZB, ODF4, PLAU, OLR1, GNG7, and DTHD1) were independent prognostic factors related to OS in patients with HNSCC. The gene discussed is HOXB9; the disease is head and neck squamous cell carcinoma.