Table 2.
Comparative performance of six variants for MIPA in their ability to (i) produce small P-values for the relevant gene sets (Sensitivity), (ii) rank close to the top these context-relevant gene sets (Prioritization) and (iii) not generate more false positive rates than expected (Specificity)
| Method | P-value (sensitivity) | % Rank (prioritization) | False positive rate (specificity) | |||
|---|---|---|---|---|---|---|
| Median | Mean | Median | Mean | 1% | 5% | |
| MIPA_var_1 | 0.0025 | 0.2682 | 23.5812 | 30.9202 | 2.5427 | 5.0149 |
| MIPA_var_2 | 0.0000 | 0.1132 | 3.3994 | 22.2025 | 14.2291 | 19.2215 |
| MIPA_var_3 | 0.9200 | 0.8329 | 79.4737 | 73.3134 | 0.0000 | 0.0000 |
| MIPA_var_4 | 0.0299 | 0.3079 | 44.2210 | 47.2948 | 0.7354 | 1.1496 |
| MIPA_var_5 | 0.0000 | 0.0777 | 6.2500 | 25.1189 | 27.9256 | 36.4886 |
| MIPA_var_6 | 0.7900 | 0.7152 | 64.1938 | 61.3367 | 0.0000 | 0.0001 |