TNF and cancer: To explore the potential reasons for the poor prognosis in patients with the AME3 subtype, we calculated the activity of 14 cancer-related signaling pathways, including the Androgen, Estrogen, EGFR, Hypoxia, JAK-STAT, MAPK, NFκB, PI3K, p53, TGFβ, TNFα, TRAIL, VEGF, and WNT pathways, which are available in the R package “PROGENy” (21) (Supplementary Table S1).