Table 3.
The improvement in network modeling with the addition of prior knowledge
| Data set | Simulated data | Yeast cell cycle study, benchmark from BIND | Yeast cell cycle study, benchmark from ChIP-chip | Mouse pancreas study |
|---|---|---|---|---|
| Number of genes | 76 | 107 | 107 | 36 |
| Number of established regulations | 124 | 114 | 190 | 24 |
| Number of possible regulations | 76*75 = 5700 | 107*106/2 = 5671* | 9*106 = 954 | 36*35 = 1260 |
| Number of known regulations recovered with (without) prior knowledge | 21 (14) | 26 (13) | 23 (11) | 12 (6) |
| Total number of regulations predicted, with (without) prior knowledge | 503 (440) | 436 (387) | 58 (33) | 322 (297) |
| Improvement over plain BN | χ 2 = 0.36, p~0.54 |
χ 2 = 2.28, p < 0.13 | χ 2 = 0.04, p~0.84 | χ 2 = 0.98, p~0.32 |
| Improvement: over random selection | χ 2 = 7.32, p < 0.01 |
χ 2 = 24.5, p < 0.001 | χ 2= 6.71, p < 0.01 | χ 2 = 2.87, p < 0.09 |
| Plain BN over random selection |
χ 2 = 1.58, p~0.2 |
χ 2 = 2.42, p~0.11 | χ 2 = 1.6, p~0.2 | χ 2 = 0.01, p~0.8 |
* We ignored edge direction with comparing to BIND since it contains both directed and undirected interactions.