Table 2.
Summary of prognostic gene clusters
| Prognostic gene cluster | Prognostic association | N genes | Overrepresented functions/biological themesa | Primary cell (sub)type with highest expression | Association with grade |
|---|---|---|---|---|---|
| S1 | Anti-survival | 240 | PRC1 targets, EMT, hypoxia | Ubiquitous (malignant & stroma-skewed) | N/S |
| S2 | Anti-survival | 196 | MTORC1 signaling, ribosome biogenesis, protein misfolding response | Ubiquitous (malignant-skewed) | N/S |
| S3 | Pro-survival | 140 | None | Ubiquitous (endothelial & malignant-skewed) | + |
| S4 | Anti-survival | 139 | EMT, extracellular matrix, TGFB signaling | Fibroblasts | + |
| S5 | Pro-survival | 120 | Antigen receptor-mediated antitumor immunity | T/NK cells | + |
| S6 | Pro-survival | 123 | Epithelial differentiation (overlap with cluster L2) | Well-differentiated malignant cells | - |
| L1 | Anti-LNM | 162 | Epithelial differentiation | Well-differentiated malignant cell cluster | - |
| L2 | Anti-LNM | 209 | Epithelial differentiation | Well-differentiated malignant cells | - |
| L3 | Anti-LNM | 15 | Intracellular transport, RNA splicing | Ubiquitous (malignant-skewed) | - |
| L4 | Pro-LNM | 196 | Cell cycle genes, p53-DREAM targets, DNA replication/repair | G2/M phase/stem-like malignant cells | + |
| L5 | Pro-LNM | 146 | Regulation of various immune processes, KRAS and IL2-STAT5 signaling | Ubiquitous across non-malignant cell types | + |
| L6 | Pro-LNM | 14 | RNA splicing | Ubiquitous (malignant-skewed) | + |
aIdentified by gene set overlap analysis (GSOA), detailed in Additional file 2: Table S6