Table 4.

Common interactions identified by the eight methods.

	jAM.SA	JAM.GR	DEGAS	BioNet	NetBox	ClustEx	OptDis	NetWalker
jAM.SA	2141	118	152	105	234	97	26	90
jAM.GR	0.0433	702	133	123	178	18	15	82
DEGAS	0.0446	0.0668	1421	105	256	34	27	84
BioNet	0.0397	0.1035	0.0545	609	429	39	46	173
NetBox	0.0686	0.0878	0.0960	0.2549	1503	100	94	215
ClustEx	0.0318	0.0107	0.0142	0.0248	0.0415	1004	12	51
OptDis	0.0110	0.0160	0.0164	0.0567	0.0567	0.0097	249	34
NetWalker	0.0316	0.0580	0.0394	0.1405	0.1032	0.0292	0.0337	795

Notes: The numbers on the diagonal indicate the numbers of interactions identified by the corresponding method alone. The numbers above the diagonal are the numbers of interactions found by both the indicated methods. And the numbers below the diagonal are the Jaccard similarities between the interaction sets selected by the indicated methods (similarities >0.1 are in bold).