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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
  1. aFor HIDEN we vary the maximum allowable level from three to eight. We report the adjacency and reachability penalties as well as the Z-scores for these penalties for each experiment. “Num. Level” denotes the maximum number of allowed levels. The results for HiNO on human are omitted, because of problems in execution.