In the enriched antigen presentation and integrin signaling pathways, we recognized significant roles of CALR, TAP1, HLA-DQB2, PTEN, HRAS, RHOA, ITGA3 and IT GA5 from the topological scorings and the differential gene activities in the evolving HNSCC transcriptome. Here, PTEN is linked to head and neck squamous cell carcinoma.