Our systematic groupings of CNVs provided opportunities to investigate gene pathways that may be unique or shared across DSM diagnoses or within sub-groups of these disorders. Pathway analysis identified significant biological, cellular, and molecular gene processes, some of which were shared across disorders and others were unique to given sub-groupings. We first examined enriched gene pathways in gene groups associated with each of the four DSM diagnoses separately under strict criteria (e.g. ASD, ID, schizophrenia) (Figure 3A–C and Table S3, available online). Epilepsy was excluded because of the small number of CNVs under strict criteria, only three in total. The majority of significant findings across disorders pinpointed processes at the synapse. For example, synapse processes were significant for ASD (p<.001), ID (p=.007), and schizophrenia (p=.003). In addition, synaptic transmission was significant in ASD (p<.001) and schizophrenia (p<.001). Post-synaptic membrane was highly enriched in ASD (p=.003) and ID (p=.003). Extracellular ligand-gated ion channel activity was significant in ASD (p=.002), ID (p=.02), and schizophrenia (p=.007). Also, glycerophospholipid metabolic process was noted in ID (p=.02) and schizophrenia (p=.002).
