Gene Set Enrichment for Differentially Spliced Genes in ZNF804A-Depleted Cells and De Novo Disease Variants.
| Gene set . | Observed . | Expected . | Enrichment . | P value . | P corr. . |
|---|---|---|---|---|---|
| SCZ_syn | 23 | 22 | 1.05 | .444 | ns |
| SCZ_mis | 53 | 49.4 | 1.07 | .321 | ns |
| SCZ_LoF | 10 | 7.4 | 1.35 | .211 | ns |
| ASD_syn | 94 | 85.7 | 1.1 | .197 | ns |
| ASD_mis | 254 | 192.1 | 1.32 | 1.16 × 10–5 | 1.39 × 10–4 |
| ASD_LoF | 62 | 28.8 | 2.16 | 5.21 × 10–8 | 6.25 × 10–7 |
| ID_syn | 3 | 4.1 | 0.727 | .78 | ns |
| ID_mis | 16 | 9.3 | 1.73 | .03 | ns |
| ID_LoF | 5 | 1.4 | 3.61 | .01 | ns |
| control_syn | 51 | 44 | 1.16 | .17 | ns |
| control_mis | 109 | 98.8 | 1.1 | .16 | ns |
| control_LoF | 20 | 14.8 | 1.35 | .11 | ns |
| Gene set . | Observed . | Expected . | Enrichment . | P value . | P corr. . |
|---|---|---|---|---|---|
| SCZ_syn | 23 | 22 | 1.05 | .444 | ns |
| SCZ_mis | 53 | 49.4 | 1.07 | .321 | ns |
| SCZ_LoF | 10 | 7.4 | 1.35 | .211 | ns |
| ASD_syn | 94 | 85.7 | 1.1 | .197 | ns |
| ASD_mis | 254 | 192.1 | 1.32 | 1.16 × 10–5 | 1.39 × 10–4 |
| ASD_LoF | 62 | 28.8 | 2.16 | 5.21 × 10–8 | 6.25 × 10–7 |
| ID_syn | 3 | 4.1 | 0.727 | .78 | ns |
| ID_mis | 16 | 9.3 | 1.73 | .03 | ns |
| ID_LoF | 5 | 1.4 | 3.61 | .01 | ns |
| control_syn | 51 | 44 | 1.16 | .17 | ns |
| control_mis | 109 | 98.8 | 1.1 | .16 | ns |
| control_LoF | 20 | 14.8 | 1.35 | .11 | ns |
Note: Statistical enrichment for de novo variants in schizophrenia (SCZ), autism spectrum disorder (ASD), and intellectual disability (ID) and differentially spliced genes in ZNF804A-depleted cells. De novo variants were collated from Fromer et al54 and Genovese et al.42 Tests for enrichment were conducted using denovolyzeR.43 Initial P values were corrected (P corr.) for multiple testing (Bonferroni). Only corrected P values < .05 were considered statistically significant. ns, not significant.
Gene Set Enrichment for Differentially Spliced Genes in ZNF804A-Depleted Cells and De Novo Disease Variants.
| Gene set . | Observed . | Expected . | Enrichment . | P value . | P corr. . |
|---|---|---|---|---|---|
| SCZ_syn | 23 | 22 | 1.05 | .444 | ns |
| SCZ_mis | 53 | 49.4 | 1.07 | .321 | ns |
| SCZ_LoF | 10 | 7.4 | 1.35 | .211 | ns |
| ASD_syn | 94 | 85.7 | 1.1 | .197 | ns |
| ASD_mis | 254 | 192.1 | 1.32 | 1.16 × 10–5 | 1.39 × 10–4 |
| ASD_LoF | 62 | 28.8 | 2.16 | 5.21 × 10–8 | 6.25 × 10–7 |
| ID_syn | 3 | 4.1 | 0.727 | .78 | ns |
| ID_mis | 16 | 9.3 | 1.73 | .03 | ns |
| ID_LoF | 5 | 1.4 | 3.61 | .01 | ns |
| control_syn | 51 | 44 | 1.16 | .17 | ns |
| control_mis | 109 | 98.8 | 1.1 | .16 | ns |
| control_LoF | 20 | 14.8 | 1.35 | .11 | ns |
| Gene set . | Observed . | Expected . | Enrichment . | P value . | P corr. . |
|---|---|---|---|---|---|
| SCZ_syn | 23 | 22 | 1.05 | .444 | ns |
| SCZ_mis | 53 | 49.4 | 1.07 | .321 | ns |
| SCZ_LoF | 10 | 7.4 | 1.35 | .211 | ns |
| ASD_syn | 94 | 85.7 | 1.1 | .197 | ns |
| ASD_mis | 254 | 192.1 | 1.32 | 1.16 × 10–5 | 1.39 × 10–4 |
| ASD_LoF | 62 | 28.8 | 2.16 | 5.21 × 10–8 | 6.25 × 10–7 |
| ID_syn | 3 | 4.1 | 0.727 | .78 | ns |
| ID_mis | 16 | 9.3 | 1.73 | .03 | ns |
| ID_LoF | 5 | 1.4 | 3.61 | .01 | ns |
| control_syn | 51 | 44 | 1.16 | .17 | ns |
| control_mis | 109 | 98.8 | 1.1 | .16 | ns |
| control_LoF | 20 | 14.8 | 1.35 | .11 | ns |
Note: Statistical enrichment for de novo variants in schizophrenia (SCZ), autism spectrum disorder (ASD), and intellectual disability (ID) and differentially spliced genes in ZNF804A-depleted cells. De novo variants were collated from Fromer et al54 and Genovese et al.42 Tests for enrichment were conducted using denovolyzeR.43 Initial P values were corrected (P corr.) for multiple testing (Bonferroni). Only corrected P values < .05 were considered statistically significant. ns, not significant.
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