Table 1.

Estimated threshold for each method by dataset, with methods sorted by the sum of absolute deviations from the GO functional similarity threshold.

Method	Anoxia	Reoxygenation	Alpha	Absolute deviations from GO threshold
GO Functional Similarity	0.97	0.92	0.85
Spectral Clustering	0.93	0.97a	0.89	0.04+0.05+0.04 = 0.13
Maximal Clique-2	0.90	0.91	0.74	0.07+0.01+0.11 = 0.19
Power	0.88	0.94	0.96	0.09+0.02+0.11 = 0.22
Bonferroni adjustment	0.85	0.93	0.95	0.12+0.01+0.10 = 0.23
Control-Spot	0.93	0.83	0.70	0.04+0.09+0.15 = 0.28
Maximal Clique-3	0.87	0.89	0.60	0.10+0.03+0.25 = 0.38
Top 1 Percent	0.81	0.81	0.72	0.16+0.11+0.13 = 0.40

^aThresholds above the GO functional similarity threshold are in bold.