Extended Data Table 1. ALIGATOR and INRICH.
Gene sets that have been reported to be enriched for schizophrenia associations and or rare mutations were tested for enrichment for genome wide significant associations using ALIGATOR44 and INRICH45. Specifically, we tested the glutamatergic postsynaptic proteins comprising activity-regulated cytoskeleton-associated protein (ARC) and N-methyl-d-aspartate receptor (NMDAR) complexes33-35, other curated synaptic gene-sets14,51, targets of fragile X mental retardation protein (FMRP) 33-35, calcium channels 11,33, and TargetScan predicted MIR137 sets11,16. The MIR137 TargetScan sets contain computationally predicted conserved miRNA target sites in 3′UTRs of human genes52. The current version is v6, but the version used in the prior PGC SCZ report16 was based on v5 (filtered for a probability of conserved targeting > 0.9). We report the results of both analyses for consistency with previous work. The association at the extended MHC complex was not included given the extensive linkage disequilibrium at this region spans large numbers of genes. NA means that the pathway in question contained fewer than 2 significant genes (for ALIGATOR) or regions (INRICH).
| SET | ALIGATOR | INRICH |
|---|---|---|
| Postsynaptic sets | ||
| ARC | NA | 1 |
| NMDAR | NA | 0.458 |
|
| ||
| Curated pre- and postsynaptic sets | ||
| Cell adhesion and trans8 synaptic signalling | 0.902 | 0.44 |
| Structural plasticity | NA | NA |
| Excitability | NA | NA |
|
| ||
| FMRP sets | ||
| FMRP | 0.0066 | 5.00E-05 |
|
| ||
| MIR137 sets | ||
| Targetscan v5 with PCT > 0.9 | 0.0371 | 0.0103 |
| Targetscan v6.2 | 0.059 | 0.0024 |
|
| ||
| Calcium signalling sets | ||
| CACN* channel subunits | 0.0338 | 0.022 |