Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders

Hoang T. Nguyen; Julien Bryois; April Kim; Amanda Dobbyn; Laura M. Huckins; Ana B. Munoz-Manchado; Douglas M. Ruderfer; Giulio Genovese; Menachem Fromer; Xinyi Xu; Dalila Pinto; Sten Linnarsson; Matthijs Verhage; August B. Smit; Jens Hjerling-Leffler; Joseph D. Buxbaum; Christina Hultman; Pamela Sklar; Shaun M. Purcell; Kasper Lage; Xin He; Patrick F. Sullivan; Eli A. Stahl

doi:10.1186/s13073-017-0497-y

Table 2 Enrichment of known gene sets from extTADA results for schizophrenia

From: Integrated Bayesian analysis of rare exonic variants to identify risk genes for schizophrenia and neurodevelopmental disorders

Gene set	Gene number	Overlapping gene number	p value	FDR
Constrained	1003	939	3.3e-06	6.2e-04
pLI09	3488	3241	1.0e-05	8.2e-04
rbfox2	3068	2895	1.3e-05	8.2e-04
chd8.human_brain	2798	2601	5.0e-05	2.3e-03
rbfox13	3445	3230	1.7e-04	6.3e-03
FMRP_targets	839	792	2.1e-04	6.5e-03
celf4	2675	2468	2.7e-04	7.1e-03
Module.M3	162	145	5.6e-04	1.3e-02
DD.allDenovoMiDandLoF	1271	1271	7.0e-04	1.4e-02
ARC	28	25	1.0e-03	1.8e-02
NMDAR_network	61	58	1.5e-03	2.3e-02
abnormal_emotionORaffect_behavior	392	363	1.5e-03	2.3e-02
AlleleBiasedExpression.Neuron	802	619	1.9e-03	2.6e-02
Module.M13	149	129	2.0e-03	2.6e-02
abnormal_cued_conditioning_behavior	74	67	2.5e-03	2.9e-02
mGluR5	39	36	2.4e-03	2.9e-02
abnormal_sensory_capabilitiesORreflexesORnociception	607	579	4.5e-03	4.9e-02
mir137	3260	2940	7.0e-03	6.5e-02
abnormal_behavior	2037	1937	7.0e-03	6.5e-02
Pardinas2017_extTable9	534	522	7.0e-03	6.5e-02
PSD-95_(core)	65	57	8.0e-03	6.7e-02
abnormal_excitatory_postsynaptic_currents	73	67	8.0e-03	6.7e-02
list.EPI.43genes.2017.Epi4K.2017	43	38	9.2e-03	7.2e-02
abnormal_socialORconspecific_interaction	257	238	9.4e-03	7.2e-02
abnormal_associative_learning	204	190	1.5e-02	1.1e-01
abnormal_social_investigation	64	54	1.8e-02	1.2e-01
Module.M1	1244	1071	1.8e-02	1.2e-01
synaptome	1887	1816	1.9e-02	1.3e-01
abnormal_motor_capabilitiesORcoordinationORmovement	1398	1326	2.0e-02	1.3e-01
CYFIP1_all	37	34	2.1e-02	1.3e-01
abnormal_fearORanxiety-related_behavior	232	213	2.3e-02	1.4e-01
abnormal_behavioral_response_to_xenobiotic	219	208	3.0e-02	1.7e-01
abnormal_learningORmemoryORconditioning	449	414	3.1e-02	1.7e-01
abnormal_brain_size	193	180	3.6e-02	1.8e-01
abnormal_contextual_conditioning_behavior	95	88	3.4e-02	1.8e-01
abnormal_excitatory_postsynaptic_potential	64	58	3.5e-02	1.8e-01
abnormal_aggression-related_behavior	69	62	3.7e-02	1.8e-01
Module.M2	38	35	4.1e-02	2.0e-01
abnormal_discrimination_learning	21	20	4.3e-02	2.0e-01

These p values were obtained from 10,000,000 simulations, and then adjusted using the method of [58]. The information for these gene sets is summarized in Additional file 1: Table S2. The second column (Gene number) shows the number of genes in the gene set. The third column shows the number of overlapping genes between the gene sets and the 19,358 genes used by extTADA.
FDR false discovery rate

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