The function of communities in protein interaction networks at multiple scales

Lewis, Anna CF; Jones, Nick S; Porter, Mason A; Deane, Charlotte M

doi:10.1186/1752-0509-4-100

BMC Systems Biology

Table 4 Topological metrics tested and AUCs

From: The function of communities in protein interaction networks at multiple scales

	A			P
Network topology measure	G	C	M	G	C	M
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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ISSN: 1752-0509

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