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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
  1. 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.
  2. FDR false discovery rate
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Genome Medicine

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