Table 4 |
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|
Topological metrics tested and AUCs |
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|
A |
P |
|||||
|
Network topology measure |
G |
C |
M |
G |
C |
M |
|
|
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|
Mean degree |
0.6476 |
0.6476 |
0.6142 |
0.5130 |
0.5373 |
0.5387 |
|
Degree assortativity coefficient [58] |
0.6913 |
0.6913 |
0.6277 |
0.4799 |
0.5517 |
0.5181 |
|
Clustering coefficient [59] |
0.7186 |
0.7186 |
0.6613 |
0.5521 |
0.5829 |
0.5725 |
|
Global mean Soffer clustering coefficient [60] |
0.4857 |
0.4857 |
0.4819 |
0.3915 |
0.4735 |
0.4461 |
|
Local mean Soffer clustering coefficient [60] |
0.4784 |
0.4784 |
0.4662 |
0.3892 |
0.4654 |
0.4540 |
|
Mean geodesic node betweenness centrality [61] |
0.4600 |
0.4600 |
0.4973 |
0.5045 |
0.5094 |
0.4959 |
|
Mean closeness centrality [61] |
0.5275 |
0.5275 |
0.5524 |
0.4877 |
0.4919 |
0.4815 |
|
Mean eigenvector centrality [61] |
0.5601 |
0.5601 |
0.5722 |
0.5312 |
0.5551 |
0.5246 |
|
Mean information centrality [61] |
0.5191 |
0.5191 |
0.5429 |
0.5253 |
0.5456 |
0.5170 |
|
Mean geodesic distance [59] |
0.3839 |
0.3839 |
0.3717 |
0.4274 |
0.4945 |
0.5066 |
|
Diameter [61] |
0.4457 |
0.4457 |
0.4042 |
0.4366 |
0.5004 |
0.5079 |
|
Mean harmonic geodesic distance [59] |
0.4088 |
0.4088 |
0.4042 |
0.5024 |
0.4834 |
0.4995 |
|
Energy [59] |
0.5237 |
0.5237 |
0.4982 |
0.4568 |
0.4976 |
0.5114 |
|
Entropy [59] |
0.5655 |
0.5655 |
0.5327 |
0.5077 |
0.5127 |
0.5280 |
|
Off-diagonal complexity [62] |
0.5941 |
0.5941 |
0.5457 |
0.5081 |
0.5054 |
0.5237 |
|
Cyclomatic number [62] |
0.6331 |
0.6331 |
0.5733 |
0.5173 |
0.5300 |
0.5425 |
|
Connectivity [62] |
0.6437 |
0.6437 |
0.5766 |
0.5245 |
0.5334 |
0.5468 |
|
Number of spanning trees [62] |
0.4525 |
0.4525 |
0.4531 |
0.4451 |
0.4516 |
0.4491 |
|
Medium articulation [62] |
0.5659 |
0.5659 |
0.4463 |
0.5295 |
0.5070 |
0.5592 |
|
Efficiency complexity [62] |
0.5316 |
0.5316 |
0.5343 |
0.4911 |
0.4945 |
0.4982 |
|
Graph index complexity [62] |
0.6564 |
0.6564 |
0.6492 |
0.5211 |
0.5469 |
0.5250 |
|
Density |
0.6541 |
0.6541 |
0.6553 |
0.5277 |
0.5676 |
0.5235 |
|
Efficiency [63] |
0.5790 |
0.5790 |
0.5896 |
0.4964 |
0.5071 |
0.4865 |
|
Fraction of articulation vertices [64] |
0.5065 |
0.5065 |
0.5028 |
0.5216 |
0.5062 |
0.5091 |
|
Largest eigenvalue |
0.6054 |
0.6054 |
0.5663 |
0.4941 |
0.5041 |
0.5185 |
|
Rich club coefficient [65] |
0.5428 |
0.5428 |
0.5896 |
0.4988 |
0.5209 |
0.4868 |
|
|
||||||
|
The network topology measures tested and their associated AUCs. We report the results for using each of these as a predictor for functional homogeneity as judged under the three measures of functional similarity (GO, G, correlated growth rates, C, and MIPS, M) for both the A and P networks. The AUCs are given as the average performance over the range 0 ≤ log(λ) ≤ 3. The clustering coefficient (definition given in the text, equation 9) is the best predictor in all cases. (The topological properties were computed from code developed by Gabriel Villar.) |
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|
Lewis et al. BMC Systems Biology 2010 4:100 doi:10.1186/1752-0509-4-100 |
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