Table 3. Fifty-eight network nodes with significant raw and topology-substracted P values (≤0.05) after seeding with 157 genes from whole-genome AD linkage scan.

Rank*	Sec. ev.	P valuer	SP ID	Symbol	P valuets	MLS	Rank	Sec. ev.	P valuer	SP ID	Symbol	P valuets	MLS
7	173.20	0.0012	P16220	CREB1	0.0237		124	155.81	0.0217	P45983	MAPK8	0.0109	1.8
9	172.31	0.0014	P43320	CRYBB2	0.0463		131	155.41	0.0229	P19174	PLCG1	0.0226
10	172.20	0.0015	P00750	PLAT	0.0086		136	154.74	0.0251	Q03405	PLAUR	0.0031	7.70
14	171.21	0.0018	P02593	CALM3	0.0397	7.7	137	154.73	0.0251	P08519	LPA	0.0291	2.20
15	171.21	0.0018	P20226	TBP	0.0306	2.2	143	154.29	0.0266	P06858	LPL	0.0049
19	169.74	0.0024	P17080	RAN	0.0020		147	154.06	0.0274	P10451	SPP1	0.0394
23	169.03	0.0028	P11498	PC	0.0243		151	153.91	0.0280	P45985	MAP2K4	0.0194
31	166.92	0.0041	Q13510	ASAH1	0.0091		154	153.41	0.0299	Q05586	GRIN1	0.0280
41	163.48	0.0074	P15498	VAV1	0.0437		156	153.14	0.0310	P04629	NTRK1	0.0414
42	162.77	0.0082	P05231	IL6	0.0466		162	153.03	0.0315	P26651	ZFP36	0.0091	7.7
45	162.63	0.0084	P06744	GPI	0.0051		166	152.79	0.0325	Q05682	CALD1	0.0046
53	161.26	0.0103	Q9NZ50	SR	0.0349		167	152.70	0.0329	P21359	NF1	0.0294
54	161.22	0.0103	P02649	APOE	0.0026	7.7	171	152.56	0.0335	P06729	CD2	0.0149
62	160.64	0.0112	P32119	PRDX2	0.0377		176	152.44	0.0340	P25098	ADRBK1	0.0406
66	160.35	0.0117	P29474	NOS3	0.0437		182	152.02	0.0359	P35520	CBS	0.0037
70	159.54	0.0131	Q14289	PTK2B	0.0314		184	151.98	0.0362	Q9NT12	ATP8A2	0.0177
75	158.61	0.0149	P01266	TG	0.0329		185	151.96	0.0362	P46734	MAP2K3	0.0049
78	158.56	0.0150	P08133	ANXA6	0.0157		191	151.71	0.0374	P19338	NCL	0.0477
94	157.72	0.0168	P10145	IL8	0.0057		195	151.63	0.0378	P11137	MAP2	0.0106
97	157.52	0.0173	Q00403	GTF2B	0.0497	1.6	199	151.61	0.0379	P08571	CD14	0.0111
100	157.42	0.0175	P11912	CD79A	0.0034	7.7	206	151.32	0.0394	Q9UIT9	MYLK	0.0163
109	156.76	0.0191	P07204	THBD	0.0191		210	151.05	0.0408	P09601	HMOX1	0.0400
110	156.67	0.0193	P16333	NCK1	0.0437		211	151.03	0.0409	P18206	VCL	0.0117	1.8
111	156.63	0.0195	P00749	PLAU	0.0026	1.8	220	150.73	0.0425	P42261	GRIA1	0.0100
112	156.62	0.0195	Q92934	BAD	0.0483		224	150.67	0.0429	P11166	SLC2A1	0.0203
115	156.38	0.0201	P47712	PLA2G4A	0.0214		236	150.36	0.0446	O95644	NFATC1	0.0451
117	156.25	0.0205	Q02750	MAP2K1	0.0449		245	149.93	0.0471	P00374	DHFR	0.0351
118	156.24	0.0205	P55290	CDH13	0.0394		248	149.86	0.0476	P02753	RBP4	0.0280
120	156.02	0.0211	P56945	BCAR1	0.0426		252	149.67	0.0487	P12270	TPR	0.0400

Bold, nodes with primary evidence; italics, AD expert genes; P value_r, raw P value; P value_ts, topology-subtracted P value; SP ID, Swiss Prot identifier; Sec. ev., secondary evidence value.

^*Sorted by raw P values.