Table 2.
Degree of overlap between the signatures of different cancer types measured at the optimal tunings
| BRCA |
GBM |
LAML |
LUSC |
SKCM |
|||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| I | R | RR | C | R2 | I | R | RR | C | R2 | I | R | RR | C | R2 | I | R | RR | C | R2 | I | R | RR | C | R2 | |
| BRCA | 0.000 | 0.037 | 1/27 | 0.490 | 0.000 | 0.000 | 0.049 | 2/41 | 0.359 | 0.000 | 0.000 | 0.100 | 1/10 | 0.286 | 0.000 | 0.000 | 0.023 | 1/44 | 0.360 | 0.000 | |||||
| 0.000 | 0.025 | 1/40 | 0.450 | 0.025 | 0.097 | 0.118 | 8/68 | 0.524 | 0.325 | 0.127 | 0.119 | 8/67 | 0.474 | 0.275 | 0.021 | 0.044 | 2/45 | 0.450 | 0.075 | ||||||
| 0.000 | 0.029 | 1/34 | 0.450 | 0.000 | 0.000 | 0.100 | 1/10 | 0.455 | 0.000 | 0.000 | 0.125 | 1/8 | 0.636 | 0.000 | 0.000 | 0.045 | 1/22 | 0.600 | 0.000 | ||||||
| GBM | 0.000 | 0.037 | 1/27 | 0.396 | 0.000 | 0.000 | 0.033 | 2/61 | 0.365 | 0.250 | 0.000 | 0.107 | 3/28 | 0.440 | 0.000 | 0.000 | 0.032 | 2/63 | 0.392 | 0.333 | |||||
| 0.000 | 0.025 | 1/40 | 0.283 | 0.000 | 0.000 | 0.025 | 1/40 | 0.427 | 0.333 | 0.000 | 0.026 | 1/39 | 0.392 | 0.333 | 0.091 | 0.200 | 2/10 | 0.296 | 0.333 | ||||||
| 0.000 | 0.034 | 1/29 | 0.225 | 0.000 | 0.000 | 0.028 | 1/36 | 0.352 | 0.150 | 0.020 | 0.057 | 2/35 | 0.248 | 0.150 | 0.016 | 0.067 | 3/45 | 0.243 | 0.250 | ||||||
| LAML | 0.000 | 0.024 | 1/42 | 0.154 | 0.000 | 0.000 | 0.068 | 4/59 | 0.186 | 0.077 | 0.000 | 0.022 | 1/45 | 0.293 | 0.000 | 0.000 | 0.053 | 4/76 | 0.215 | 0.179 | |||||
| 0.097 | 0.158 | 9/57 | 0.272 | 0.410 | 0.000 | 0.029 | 1/35 | 0.248 | 0.000 | 0.145 | 0.161 | 9/56 | 0.280 | 0.385 | 0.043 | 0.105 | 4/38 | 0.256 | 0.154 | ||||||
| 0.000 | 0.200 | 1/5 | 0.182 | 0.000 | 0.000 | 0.120 | 3/25 | 0.536 | 0.727 | 0.000 | 0.125 | 1/8 | 0.421 | 0.000 | 0.000 | 0.059 | 1/17 | 0.553 | 0.364 | ||||||
| LUSC | 0.000 | 0.100 | 1/10 | 0.179 | 0.000 | 0.000 | 0.033 | 1/30 | 0.143 | 0.000 | 0.000 | 0.070 | 3/43 | 0.114 | 0.143 | 0.000 | 0.043 | 2/46 | 0.153 | 0.000 | |||||
| 0.127 | 0.167 | 10/60 | 0.283 | 0.425 | 0.000 | 0.054 | 2/37 | 0.375 | 0.050 | 0.145 | 0.197 | 12/61 | 0.321 | 0.450 | 0.043 | 0.071 | 3/42 | 0.281 | 0.075 | ||||||
| 0.000 | 0.028 | 1/7 | 0.000 | 0.000 | 0.020 | 0.086 | 3/35 | 0.120 | 0.909 | 0.000 | 0.077 | 1/13 | 0.041 | 0.000 | 0.029 | 0.083 | 2/24 | 0.207 | 0.364 | ||||||
| SKCM | 0.000 | 0.023 | 1/44 | 0.293 | 0.000 | 0.000 | 0.066 | 4/61 | 0.298 | 0.024 | 0.000 | 0.013 | 1/79 | 0.268 | 0.073 | 0.000 | 0.043 | 2/46 | 0.373 | 0.000 | |||||
| 0.021 | 0.043 | 2/47 | 0.742 | 0.444 | 0.091 | 0.333 | 3/9 | 0.704 | 0.111 | 0.043 | 0.067 | 3/45 | 0.735 | 0.667 | 0.043 | 0.065 | 3/46 | 0.792 | 0.556 | ||||||
| 0.000 | 0.048 | 1/21 | 0.520 | 0.080 | 0.016 | 0.040 | 2/50 | 0.427 | 0.480 | 0.000 | 0.069 | 2/29 | 0.309 | 0.000 | 0.029 | 0.077 | 2/26 | 0.469 | 0.280 | ||||||
Note. I, R, RR, C and R2 correspond to the index-based, rank-based, rank ratio, correlation-based and R-squared based measures, respectively. In each cell, rows 1–3 correspond to gene expression, methylation and CNA.