Table 2.

Enriched CNS Gene Sets, Combined Analysis

	Ngene	Combined			Deletion		Duplication
		p	Padj	OR (95% CI)	p	Padj	p	Padj
NMDAR network	59	4.3×10−9	1.7×10−6	2.47 (1.8–3.44)	0.045	1	2.5×10−9	1.0×10−6
GABAA	15	3.0×10−6	0.0012	2.51 (1.65–3.97)	0.00068	0.27	5.4×10−5	0.022
Abnormal associative learning	193	1.6×10−5	0.0066	1.38 (1.19–1.61)	1.0	1	1.6×10−10	6.2×10−8
Abnormal long-term potentiation	145	2.0×10−5	0.0081	1.49 (1.24–1.8)	0.58	1	1.1×10−6	0.00044
Abnormal behavior	1,973	5.1×10−5	0.020	1.12 (1.06–1.19)	3.0×10−6	0.0012	0.05	1
Abnormal CNS synaptic transmission	371	5.5×10−5	0.022	1.22 (1.11–1.35)	5.1×10−6	0.002	0.12	1
Thin cerebral cortex	45	0.00018	0.071	1.91 (1.32–2.8)	0.12	1	0.0006	0.24
Abnormal consumption behavior	442	0.00019	0.077	1.24 (1.09–1.41)	0.059	1	0.0005	0.2
Abnormal cued conditioning behavior	68	0.00027	0.11	1.69 (1.24–2.35)	0.55	1	1.4×10−5	0.0055
Abnormal synaptic transmission	437	0.00027	0.11	1.18 (1.08–1.29)	1.1×10−5	0.0044	0.21	1
Abnormal learning/memory/conditioning	424	0.00031	0.12	1.18 (1.08–1.29)	7.3×10−5	0.029	0.089	1
PSD-95 (core)	58	0.00048	0.19	1.71 (1.28–2.28)	4.3×10−11	1.7×10−8	0.97	1
Abnormal contextual conditioning behavior	89	0.00061	0.24	1.53 (1.18–1.99)	0.52	1	0.00011	0.045

CNS gene sets with P_uncorrected < 0.001 in the combined analysis of deletions and duplications are listed along with the number of genes in each set, N_gene; uncorrected (p) and Bonferroni-corrected (P_adj) p values for enrichment in case CNVs; estimated odds ratios (OR); and p values for enrichment in case deletions and duplications when analyzed separately. Note that while the NMDAR network was analyzed prior to other terms in this table, here it is corrected for the same number of tests as other terms for ease of comparison. See also Tables S1 and S3.