Table 1

Comparison of HIDEN with three other methods on different 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

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.

Gülsoy et al.

Gülsoy et al. BMC Bioinformatics 2012 13:250   doi:10.1186/1471-2105-13-250

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