Fig. 3: Cluster-level SNP-heritability enrichment for schizophrenia (scz2022).

A tSNE plot from Siletti et al. colored by the significance of cluster-level SNP-heritability enrichment for scz2022. One-sided P value was calculated based on the LDSC coefficient z-score, and we calculated FDR to account for multiple comparison. Gray indicates non-significance (FDR > 0.05). Abbreviations correspond to neuronal supercluster names in Fig. 2A. B Top 25 most significant clusters with enriched of scz2022 SNP-heritability out of 199 FDR significant clusters (Supplementary Data 7), same P-value and color definitions as in Fig. 3A. C Treemap plot for key GO-CC pathways in the top 25 scz2022 clusters. We evaluated gene set enrichment for the TDEP genes in each of the top 25 significant clusters, using hypergeometric test with one-sided P-value calculated. Significantly enriched pathways (P ≤ 0.05) in all the explored clusters were integrated to highlight higher level functions. The treemap for GO-BP and GO-MF for these clusters are shown in Supplementary Fig. 7. D–E tSNE plot of clusters that remained significant for scz2022 after conditioning on bip2021 (D) and IQ (E). One-sided P value was calculated based on the LDSC coefficient z-score, and we calculated FDR to account for multiple comparison. The color scale and the tSNE coordinates are the same as in Fig. 3A ; gray dots are cells of non-significance clusters (FDR > 0.05). More cell types became insignificant when conditioned on bipolar disorder compared to when conditioned on IQ, suggesting the shared cell types might contribute via similar mechanisms to schizophrenia and bipolar but contribute via distinct mechanisms to schizophrenia and IQ.