Table 1 Comparison of HIDEN with three other methods on different networks
From: HIDEN: Hierarchical decomposition of regulatory networks
Organism | Method | Num. | Adjacency | Reachability | ||
|---|---|---|---|---|---|---|
Level | Penalty | Z-score | Penalty | Z-score | ||
Yeast | HIDEN | 3 | 140 | 10.8 | 3600 | 13.9 |
4 | 103 | 10.8 | 3027 | 14.6 | ||
5 | 88 | 9.5 | 2774 | 14.1 | ||
6 | 91 | 10.2 | 2573 | 13.4 | ||
7 | 79 | 9.8 | 2469 | 12.8 | ||
8 | 79 | 11.6 | 2365 | 13.7 | ||
vertex sort | 9 | 179 | 7.3 | 3920 | 10.2 | |
BFS-level | 4 | 245 | 6.0 | 5734 | 9.9 | |
HiNO | 3 | 279 | 6.8 | 6205 | 10.5 | |
E. coli | HIDEN | 3 | 15 | 6.3 | 19 | 7.1 |
4 | 8 | 6.5 | 10 | 6.8 | ||
5 | 5 | 6.4 | 7 | 6.7 | ||
6 | 5 | 6.2 | 6 | 6.6 | ||
7 | 5 | 6.2 | 5 | 6.6 | ||
8 | 5 | 6.2 | 5 | 6.6 | ||
vertex sort | 6 | 10 | 5.7 | 11 | 6.5 | |
BFS-level | 4 | 44 | 3.7 | 65 | 5.1 | |
HiNO | 4 | 41 | 4.2 | 59 | 5.3 | |
Human | HIDEN | 3 | 101 | 7.4 | 1950 | 9.4 |
4 | 84 | 7.4 | 1608 | 10.6 | ||
5 | 75 | 7.9 | 1435 | 10.8 | ||
6 | 66 | 7.9 | 1347 | 10.2 | ||
7 | 72 | 7.5 | 1287 | 9.7 | ||
8 | 72 | 7.3 | 1248 | 9.9 | ||
vertex sort | 5 | 207 | 1.2 | 2162 | 5.8 | |
BFS-level | 3 | 210 | 0.72 | 2163 | 6.0 | |