Table 1. Dominant and dormant driver NR genes from TCGA dataset.
Gene expression of those NRs included in the TCGA analysis on high-grade serous ovarian cancers was analyzed using a “tight clustering” algorithm (see methods section) and identified five patient clusters based on differential gene expression. Driver genes of each cluster were investigated with the gene-dominant and gene-dormant index method (21). This method extends the signal to noise ratio to identify features as either dominant or dormant in a specific cluster compared to the other clusters. The associated table identifies those genes included in the analysis and whether the gene of interest is considered dominant or dormant for each of the 5 clusters. Statistically significant drivers are highlighted.
| Nuclear Receptor | Cluster (Dominant) | p-value | Cluster (Dormant) | p-value |
|---|---|---|---|---|
| AR | 5 | 0.1917 | 1 | 0.1431 |
| ESR1 | 4 | 0.1938 | 1 | 0.7332 |
| ESRRA | 3 | 0.5610 | 2 | 0.0001 |
| HNF4A | 3 | <0.0001 | 5 | 0.1358 |
| NR1D2 | 5 | <0.0001 | 3 | 0.0119 |
| NR1H2 | 3 | 0.0220 | 1 | 0.1246 |
| NR1H3 | 4 | 0.0488 | 2 | 0.7286 |
| NR2C1 | 2 | 0.0004 | 3 | 0.0766 |
| NR2C2 | 4 | 0.0801 | 1 | 0.5953 |
| NR2E3 | 3 | 0.0189 | 5 | 0.0006 |
| NR2F1 | 2 | 0.2902 | 4 | 0.0338 |
| NR2F2 | 2 | 0.0021 | 4 | 0.4752 |
| NR2F6 | 2 | 0.3093 | 4 | 0.6245 |
| NR3C1 | 4 | 0.1591 | 2 | <0.0001 |
| NR3C2 | 4 | <0.0001 | 2 | 0.0002 |
| NR4A1 | 1 | <0.0001 | 4 | 0.1686 |
| NR4A2 | 1 | <0.0001 | 2 | 0.2969 |
| NR4A3 | 1 | <0.0001 | 5 | 0.5827 |
| NR5A1 | 3 | 0.0077 | 5 | 0.0416 |
| NR6A1 | 3 | 0.0128 | 1 | 0.1253 |
| PGR | 2 | <0.0001 | 5 | 0.0495 |
| PPARA | 4 | 0.0071 | 2 | 0.0003 |
| PPARD | 3 | 0.0011 | 5 | 0.1183 |
| RARA | 3 | <0.0001 | 4 | 0.2198 |
| RARB | 1 | <0.0001 | 2 | 0.7096 |
| RARG | 5 | 0.0002 | 2 | 0.0292 |
| RORA | 1 | 0.8749 | 5 | 0.1937 |
| RORC | 4 | 0.3249 | 1 | 0.2564 |
| RXRA | 3 | 0.1722 | 2 | 0.0316 |
| RXRB | 2 | 0.5655 | 1 | <0.0001 |
| THRA | 2 | 0.7246 | 4 | 0.8499 |
| THRB | 4 | 0.0181 | 2 | 0.0245 |
| VDR | 1 | 0.0619 | 2 | 0.0076 |
| GPER | 3 | 0.0012 | 1 | 0.8310 |
| PGRMC1 | 2 | 0.0027 | 4 | 0.0119 |
| PGRMC2 | 4 | 0.8194 | 3 | 0.0078 |