Table 3.

Source Gene Pairs With High Target Set Similarity Correspond More Frequently to Edges in Reference Networks (ppi1, ppi2, mips, mi2, mi3)

	All pairs			Confirmed pairs
Reference network	Total-all	P ≤ 0.01	% all	Total-conf	P ≤ 0.01	% conf	Increase % conf/% al
	A	B	C	D	E	F	G
ppi1	10762	631	5.86	151	37	24.50	4.18
ppi2	5804	341	5.88	38	10	26.32	4.48
mips	1283	75	5.85	31	15	48.39	8.28
mi2	8546	474	5.55	267	63	23.60	4.25
mi3	6701	400	5.97	172	50	29.07	4.87

Columns A–C refer to all source gene pairs, where both genes are present in the particular reference network; columns D–F refer only to source gene pairs which are connected in the particular reference network (= confirmed source gene pairs). The proportion of pairs with highly similar target sets is increased between four- and eight-fold for the confirmed source gene pairs.