Table 3. Clusters and Pathways.
| Cluster 1 | Cluster 2 | Cluster 3 | ||||
| Pathway Name | Coefficient | P-value | Coefficient | P-value | Coefficient | P-value |
| Intercept | −2.95 | 0.0020 | 0.34 | 0.71 | −0.74 | 0.0010 |
| Cell Cycle (+) | −0.76 | <0.0001 | −0.70 | <0.0001 | 1.69 | <0.0001 |
| ESC | NA | NA | NA | NA | NA | NA |
| B-cell | −0.57 | 0.0023 | 0.52 | 0.0049 | NA | NA |
| T-cell | NA | NA | NA | NA | NA | NA |
| Antigen | NA | NA | 0.87 | 0.0007 | −0.47 | 0.013 |
| AKT/PI3K | NA | NA | NA | NA | −0.61 | 0.0014 |
| IGF-1 | -0.88 | <0.0001 | 0.99 | <0.0001 | NA | NA |
| Chemokine | NA | NA | NA | NA | NA | NA |
| NF-κB | NA | NA | NA | NA | NA | NA |
| Notch | NA | NA | 0.34 | 0.048 | NA | NA |
| JAK/STAT | NA | NA | 0.48 | 0.016 | NA | NA |
| Complement | 0.56 | 0.0023 | NA | NA | −0.81 | <0.0001 |
| mTOR | NA | NA | NA | NA | NA | NA |
| Cell Cycle (−) | NA | NA | NA | NA | NA | NA |
| Angiogenesis | −0.47 | 0.011 | NA | NA | 0.39 | 0.035 |
| IL-stimulatory | NA | NA | −0.28 | 0.11 | 0.40 | 0.029 |
| IL-suppressive | −0.37 | 0.030 | NA | NA | NA | NA |
| Interferon | 0.36 | 0.010 | −0.27 | 0.056 | 0.30 | 0.073 |
| EGFR | NA | NA | −0.26 | 0.11 | NA | NA |
| PDGF | NA | NA | 0.56 | 0.0007 | −0.41 | 0.016 |
| Hypoxia | 0.35 | 0.033 | NA | NA | −0.39 | 0.029 |
| PTEN | NA | NA | NA | NA | NA | NA |
| Pro-apoptosis | NA | NA | NA | NA | NA | NA |
| Anti-apoptosis | 0.40 | 0.041 | −0.46 | 0.030 | NA | NA |
| TGF-β | NA | NA | NA | NA | −0.36 | 0.045 |
| Hedgehog | NA | NA | NA | NA | NA | NA |
| Wnt | 0.38 | 0.022 | NA | NA | −0.43 | 0.015 |
| Male | NA | NA | NA | NA | −0.44 | 0.16 |
| Age | 0.032 | 0.023 | −0.030 | 0.026 | NA | NA |
| Grade | −1.49 | <0.0001 | 0.50 | 0.13 | NA | NA |
| Stage | NA | NA | NA | NA | NA | NA |
Tumors with lower levels of the cell cycle stimulatory (CC+) were more likely to be in Cluster 1 or 2, other pathways held constant. Tumors with higher levels of the IGF-1 pathway were more likely to be in Cluster 2 and less likely to be in Cluster 1. Samples with increased antigen pathway expression were more likely to be in Cluster 2 and less likely to be in Cluster 3. Tumors with increased complement pathway expression were more likely to be in Cluster 1 and less likely to be in Cluster 3. NA indicates that the variable was excluded during model selection and thus deemed unimportant.