Table 2 Association of synaptic functional gene groups with schizophrenia in the three data sets

	ISC AFFY5				ISC AFFY6				GAIN AFFY6				ALL
	N genes	N SNPs	Σ -log(P)	P_EMP	N genes	N SNPs	Σ -log(P)	P_EMP	N genes	N SNPs	Σ -log(P)	P_EMP	P_COMB
All synaptic genes	795	15 105	7102	1.0E–04	906	34 860	16 071	1.0E–04	908	35 412	16 348	1.0E–04	7.6E–11
Intracellular signal transduction	112	2350	1140	0.0061	133	5387	2590	0.0037	134	5475	2450	0.2088	0.0002
Excitability	47	1120	555	0.0233	50	2656	1238	0.1026	50	2680	1327	0.0100	0.0009
CAT signaling	69	3278	1483	0.1568	79	7866	3564	0.1181	79	7962	3888	0.0013	0.0024
Endocytosis	20	257	133	0.1000	23	576	312	0.0379	23	581	312	0.0384	0.0029
Structural plasticity	72	1169	547	0.1388	81	2463	1172	0.0599	82	2494	1171	0.0887	0.0108
GPCR signaling	31	786	395	0.0395	37	1823	879	0.0832	37	1844	823	0.3340	0.0162
‘Unknown’	45	556	266	0.1250	50	1514	786	0.0087	50	1542	641	0.7143	0.0272
Protein cluster	40	893	463	0.0160	46	2039	1001	0.0435	46	2069	840	0.8210	0.0272
Tyrosine kinase signaling	7	334	185	0.0190	7	786	352	0.3401	7	798	356	0.3802	0.0491
Cell metabolism	41	216	112	0.0581	44	473	198	0.6137	44	477	224	0.1830	0.1154
Neurotransmitter metabolism	25	258	113	0.4492	27	580	290	0.0832	27	606	274	0.3137	0.1166
Intracellular trafficking	59	455	205	0.3364	70	987	424	0.5422	69	1020	519	0.0286	0.1329
LGIC signaling	33	842	403	0.1210	35	1910	820	0.5437	35	1948	855	0.4308	0.2370
Exocytosis	68	1170	512	0.4321	78	2547	1084	0.6207	78	2589	1170	0.2500	0.4062
RPSFB	47	376	160	0.5549	62	869	403	0.1933	63	889	368	0.7077	0.4204
Ion balance/transport	35	322	129	0.7092	41	727	295	0.7088	41	751	372	0.1044	0.5266
Peptide/neurothropin signals	21	515	221	0.5124	21	1122	427	0.8919	21	1132	530	0.2133	0.6615
G-protein relay	23	208	81	0.7922	23	536	235	0.4444	23	556	228	0.6758	0.7327

Abbreviations: CAT, cell adhesion and trans-synaptic molecule; GAIN, Genetic Association Information Network; GPCR, G-protein-coupled receptor; ISC, International Schizophrenia Consortium; LGIC, ligand-gated ion channel; RPSFB, RNA and protein synthesis, folding and breakdown; SNP, single-nucleotide polymorphism; Unknown, genes that are known to be expressed in the synapse but currently have no known shared function with other genes.
All P_EMP values are based on 10 000 permutations of the data.

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