Fig. 4: Significantly differentially expressed genes among the suicide-associated genes observed from Sherlock integrative analysis.

A A heatmap of differential expression in each psychiatric disorders compared to the controls. Red and green shading indicates downregulated and upregulated expression, respectively, in the given psychiatric disorders and suicide deaths. eQTL annotation above the heatmap represents the direction of each eQTL, with red and green reflecting negative and positive beta values between gene expression, respectively, and noting that the allele for the eQTL is indicated in the box. The genetic direction for suicide annotation represents the topmost line of the figure, with purple and yellow referring to the given eQTLs direction as a risk or protective allele, respectively. For example, for CNN3 gene, eQTLs direction of A of rs9432595 (showed at B) is positive that expression tends to increase in allele A of the SNP, and this allele A was observed to be risk allele from our suicide WGS genomic analysis. B Violin plots of expression of the ten identified genes according to eQTLs generated from Genotype-Tissue Expression (GTEx) project. C A regional plot for SNX19 on chromosome 11. The Hi-C plot demonstrates chromatin interaction loops. Other lines indicate chromatin accessibility regions observed from histone modifications ChIP-seq, DNase-seq, and ATAC-seq data. Cyan colors are ChIP-seq peak regions overlapped in SNPs within the LD block of rs7925664, while gray areas do not. D Boxplot demonstrating that SNX19 was significantly upregulated in individuals with schizophrenia, suicide attempters, and suicide deaths from three independent RNA-seq datasets: (1) CommonMind Consortium (CMC) in PsychENCODE, (2) Korean mental health (KMH), and (3) suicide death dataset 1 (GEO id: GSE66937). X-axis and Y-axis refer data projects and normalized gene expression, respectively. ASD autism spectrum disorder, BD bipolar disorder, SCZ schizophrenia, SA suicide attempter, MDD major depressive disorder, SD1: Suicide death 1 (GEO id: GSE66937), and SD2: Suicide death 2 (GEO: GSE101521).