Table 2.
RP gene copy number alterations associated with t-SNE clusters
| Genes | Type | Location | Cohort | Cluster | Frequency |
|---|---|---|---|---|---|
| RPL19, RPL23 | Amplification | 17q12 | BRCA | 1 | 98.9%, 83.1% |
| RPL8, RPL30 | Amplification | 8q22 | BRCA | 3 | 100%, 97.5% |
| LIHC | 3 | 98.8%, 98.8% | |||
| PRAD | 2 | 95.1%, 97.5% | |||
| LUNG | 1 | 100%, 94.3% | |||
| SKCM | 2 | 94.2%, 88.5% | |||
| HNSC | 2 | 93.2%, 85.3% | |||
| RPS3 | Amplification | 11q13 | BRCA | 2 | 100% |
| LUNG | 5 | 90.5% | |||
| RPS16 | Amplification | 19q13 | LUNG | 6 | 100% |
| RPL13A, RPL18, RPL28, RPS5, RPS9, RPS11, RPS16, RPS19 | Deletion | 19q13 | GBMLGG | 5 | 98.8% - 99.4% |
| RPL11, RPL22, RPL5, RPS8 | Deletion | 1p | GBMLGG | 5 | 97.5% |
| RPS24 | Deletion | 10q22 | GBMLGG | 3 | 90.5% |
Some tumor clusters were significantly associated with greater incidence of copy number alterations than other tumors from the same cancer cohorts (α < 0.01); clusters with > 90% of tumors possessing a given copy number alteration are included in this table. Cancer cohorts with no tumor clusters strongly associating with a RP copy number alteration were excluded from this table