Table 2.

Spearman and Pearson correlation coefficients between similarity value and difference in annotation size as well as between variance in similarity value and difference in annotation size

Similarity measure	Spearma						Pearson
	Yeast		Synthetic GO		Synthetic HPO		Yeast		Synthetic GO		Synthetic GO
	Average	Variance	Average	Variance	Average	Variance	Average	Variance	Average	Variance	Average	Variance
GIC (Graph Information Content)	–0.895310	–0.931818	–0.999928	–0.999784	–0.999784	–0.997835	–0.875583	–0.503795	–0.964250	–0.484246	–0.963553	–0.496135
NTO (Normalized Term Overlap)	0.901443	–0.233045	0.999784	0.961833	0.999784	0.959524	0.882986	–0.192168	0.990210	0.848649	0.993038	0.849263
UI (Union Intersection)	–0.909524	–0.924459	–1.000000	–0.658658	–1.000000	–0.518687	–0.906605	–0.596963	–0.963476	–0.547645	–0.963569	–0.508495
BMA with Jiang, Conrath 1997	0.283838	–0.925830	–0.902597	–0.521861	–0.891486	–0.770130	0.074788	–0.850654	–0.834208	–0.495874	–0.848264	–0.735985
BMA with Lin 1998	0.462843	–0.674892	–0.901587	–0.552237	–0.891126	–0.731530	0.303157	–0.707318	–0.836486	–0.517670	–0.852998	–0.693744
BMA with Resnik 1995	0.578211	–0.579149	–0.901587	–0.537807	–0.891126	–0.699856	0.442458	–0.487544	–0.835991	–0.507179	–0.854007	–0.670199
BMA with Schlicker 2006	0.462843	–0.674892	–0.901587	–0.552237	–0.891126	–0.731530	0.303157	–0.707318	-0.836486	–0.517670	–0.852998	–0.693744