Based on the gene expression pattern, inhibitor analysis, and regulatory network integration analysis, we named the Cluster1–3 as: Inflammation-associated Papillary Thyroid Carcinoma Classification (IPTCC), BRAF mutation and Autophagy-related Papillary Thyroid Carcinoma Classification (BAPTCC), and Lipid metabolism-related Papillary Thyroid Carcinoma Classification (LPTCC). Here, BRAF is linked to differentiated thyroid carcinoma.