Table 1. Comparison of UNCOVER with REVEALER on REVEALER’s datasets.
| NFE2L2 activation | MEK-inhibitor | KRAS essentiality | β-catenin activation | |
|---|---|---|---|---|
|
UNCOVER(ILP) solution |
KEAP1.MC MUT | BRAF.V600E MUT | KRAS.G12 13 MUT | APC.MC MUT |
| ATP11B AMP | KRAS.G12 13 MUT | ZNF385B AMP | CTNNB1.MC MUT | |
| SPINT4 DEL | NRAS MUT | ATP8A2 AMP | SLITRK1 AMP | |
| C8orf22 AMP | ||||
| Objective value | 46.17 | 108.32 | 28.00 | 22.97 |
| IC score | 0.58 | 0.49 | 0.63 | 0.67 |
| p-value | 0.000999 | 0.000999 | 0.025974 | 0.1068931 |
| Running time (s) | 14 | 39 | 9 | 9 |
|
UNCOVER(Greedy) solution |
KEAP1.MC MUT | BRAF MUT | KRAS.G12 13 MUT | APC.MC MUT |
| ATP11B AMP | KRAS.G12 13 MUT | ZNF385B AMP | CTNNB1.MC MUT | |
| SPINT4 DEL | NRAS MUT | ATP8A2 AMP | SLITRK1 AMP | |
| C8orf22 AMP | ||||
| Objective value | 46.17 | 104.29 | 28.00 | 22.97 |
| IC score | 0.58 | 0.5 | 0.63 | 0.67 |
| Running time (s) | 15 | 35 | 9 | 8 |
|
REVEALER solution |
KEAP1.MC MUT | BRAF MUT | KRAS.G12 13 MUT | APC.MC MUT |
| LRP1B DEL | KRAS.G12 13 MUT | ZNF385B AMP | CTNNB1.MC MUT | |
| OR4F13P AMP | NRAS MUT | LINC00340 DEL | ITGBL1 AMP | |
| NUP153 MUT | ||||
| Objective value | 30.35 | 104.29 | 21.86 | 22.12 |
| IC score | 0.54 | 0.5 | 0.6 | 0.7 |
| Running time (s) | 1615 | 4965 | 1243 | 787 |
For each of the four targets (NFE2L2 activation, MEK-inhibitor, KRAS essentiality, β-catenin activation) considered in [33], the set of alterations of cardinality k reported by our ILP algorithm, by our greedy algorithm, and by REVEALER (without seeds) is reported. k is chosen as in [33]. For each pair (algorithm, target) we also report the (objective) value of our objective function for the solution, the value of the IC score (that is, the objective function used in [33]), and the running time of the algorithm for the target. For solutions found by our ILP we also report the p-value computed by permutation test using 1000 permutations.