Table 1 Intersection of functional gene sets with schizophrenia-associated genes from all genetic association studies combined (duplicate genes removed)

Functions	N	SZ N	E (N)	O (N)	E (%)	O (%)	RF	CI	Nominal P	Bonferroni corrected P
VIRND	6409	345	105	195	30.5	56.5	1.9	179–345	2.2E−16	5.1e−15***
VI	4213	345	69	139	20.1	40.3	2.0	124–345	2.2E−16	5.1e−15***
V	3249	345	53	110	15.5	31.9	2.1	96–345	2.2E−14	5.1e−13***
PV	253	345	4	35	1.2	10.1	8.4	26–345	2.2E−16	5.1e−15***
V−PV	2996	345	49	75	14.2	21.7	1.5	62–345	1.1E−04	2.5e−03*
SS	2818	345	46	69	13.4	20.0	1.5	60–345	4.3E−04	9.9e−03*
I	1673	345	27	74	7.9	21.5	2.7	61–345	4.8E−15	1.1e−13***
R	159	345	3	31	0.8	9.0	11.9	23–345	2.2E−16	5.1e−15***
Repair	3319	345	54	129	15.8	37.4	2.4	114–345	2.2E−16	5.1e−15***
ND	3211	345	53	111	15.3	32.2	2.1	97–345	3.8E−15	8.7e−14***
VI × ND	1050	345	17	57	5.0	16.5	3.3	46–345	8.8E−16	2.0e−14***
VI × Repair	1123	345	18	73	5.3	21.2	4.0	61–345	2.2E−16	5.1e−15***
V × ND	783	345	13	44	3.7	12.8	3.4	34–345	7.6E−13	1.8e−11***
V × Repair	844	345	14	59	4.0	17.1	4.3	48–345	2.2E−16	5.1e−15***
I × ND	522	345	9	37	2.5	10.7	4.3	28–345	6.1E−14	1.4e−12***
I × Repair	568	345	9	47	2.7	13.6	5.0	37–345	2.2E−16	5.1e−15***
SY	1977	345	32	91	9.4	26.4	2.8	77–345	2.2E−16	5.1e−15***
VI−ND	3163	345	52	82	15.4	23.8	1.6	69–345	1.4E−05	3.2e−04**
VI−SY	3273	345	54	76	15.6	22.0	1.4	63–345	9.8E−04	2.3e−02 NS
I−ND	1151	345	19	37	5.5	10.7	2.0	28–345	8.9E−05	2.1e−03*
I−SY	1180	345	19	38	5.6	11.0	2.0	28–345	6.9E−05	1.6e−03*
ND−VI	2161	345	36	54	10.3	15.7	1.5	43–345	1.3E−03	3.0e−02 NS
SY−VI	1037	345	17	28	4.9	8.1	1.6	20–345	7.5E−03	1.7e−01 NS

Abbreviations: CI, 95 percent confidence intervals expressed as the number of identical genes; E, expected number and percentage of intersecting genes by chance; I, ischemia-induced cerebral genes; minus sign (−), overlapping genes removed, for example, V−PV, V without PV; ND, neurodevelopmental genes; NS, not significant; O, observed number or percentage of intersecting genes; PV, perivascular genes; R, postischemic repair genes; Repair, R and ND genes combined, because ND genes are involved in postischemic repair;^{18, 19} RF, representation factor, that is, the number of intersecting genes divided by the expected number of intersecting genes under independence assumption; SS, shear stress-induced endothelial genes; SY, synaptic genes; SZ, schizophrenia-associated genes; V, vascular genes including perivascular genes; VI, vascular and ischemia genes; VIRND, vascular, ischemia and postischemic repair genes.
×, gene interaction, for example, VI × ND, interaction of VI and ND genes.
Level of significance (Bonferroni corrected): *P⩽1.0E−02; **P⩽1.0E−03; ***P⩽1.0E−06.

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