Table 4. Pathway analysis output of GO terms for genes present in all CNVs and the rare and novel CNVs of independent cases.

	GO category	No. of reference genes in the category	No. of genes in the gene set and also in the category	Expected no. in the category	Ratio of enrichment	Raw P-value	P-value adjusted for multiple testing
All CNVs	Molecular function – cyclic-nucleotide phosphodiesterase activity – GO:0004112	25	5	0.7	7.11	0.0006	0.04
All CNVs	Molecular function – acetylcholine binding – GO:0042166	13	4	0.37	10.94	0.0004	0.04
All CNVs	Molecular function – 3′,5′-cyclic-nucleotide phosphodiesterase activity – GO:0004114	24	5	0.68	7.41	0.0005	0.04
All CNVs	Cellular component – MHC protein complex – GO:0042611	38	6	1.09	5.53	0.0007	0.048
Rare and novel CNVs	Cellular component – proteasome activator complex – GO:0008537	3	2	0.02	84.21	0.0002	0.034
Rare and novel CNVs	Cellular component – nuclear inclusion body – GO:0042405	4	2	0.03	63.16	0.0004	0.034

Abbreviations: CNV, copy number variant; GO, gene ontology.

GO categories are listed that did not occur in population controls and survived multiple testing.