Fig. 4: Impact of the 22q11.2 deletion on synaptic gene expression and network activity.

a SynGO annotation for genes upregulated in neurons (p < 0.05, Wald-test, DESeq2) showing enrichment for synaptic processes (two-sided Fisher exact test). The test statistics are presented in Supplementary Data 10. b Heritability enrichment for schizophrenia after excluding the 193 genes with SynGO annotation. The p-values calculated from standard errors derived from block Jackknife as implemented in LD score regression. c MEF2C is upregulated in NPC of 22q11.2 deletion carriers (N(cases)= 19, N(controls)= 29, Wald-test from DEseq2). Data is presented in a Tukey-style boxplot with the median (Q2) and the first and the second quartiles (Q2, Q3) and error bars defined by the last data point within +/− 1.5-times the interquartile range. d Spike count (mean number of spikes in a 10 s period). The activity of neurons derived from control (green, N = 12 lines, 104 wells) is compared to neurons from cases with 22q11.2 deletion (N = 9 lines, 54 wells). Pooled data is presented as Tukey-style box plots (Q1, Q2, & Q3; whiskers extend to the most extreme data points between Q1-1.5*IQR and Q3+1.5*IQR). Significance is determined by Kruskal-Wallis test with a 5 % significance level (* = p value ≤ 0.05). e Proportion of electrodes detecting spontaneous activity, against the number of days post-induction. f The most weighted subcluster graph for protein-protein interactions (PPI) for differentially expressed genes in neurons.