Fig. 1

Characterization of differential gene expression profiles in the suicidal habenula (Hb) with major depression. a Volcano plot for Hb gene expression levels in suicides and unaffected controls. Differentially expressed genes (DEGs), defined by p < 0.05, are shown in yellow (FC < = 1.2) or orange/red (FC > 1.2) circles. b Venn diagram for comparison of the 251 main DEGs and psychiatric disease-associated genes curated by the PsyGeNET database. Numerals in parenthesis indicate numbers of genes with p < 0.05 between groups with regardless of FC. Disease-associated genes are listed below the Venn diagram and categorized into several groups according to their major subcellular localization (PM: plasma membrane; NUC: nucleus; ExC: extracellular space). Genes in red characters constitute cell–cell junctions; genes in blue represent components of or interacting with extracellular matrix; and genes in green are membrane receptors and their accessory proteins. c Association between the PsyGeNET disease terms (red symbols) and disease-associated DEGs (blue). d Summary of cell-type enrichment analysis of the main 251 DEGs (EC: endothelial cell; EP: ependymal cell; MC: mural cell; NEU: neuron, AC: astrocyte, OL: oligodendrocyte lineage cell, MG: microglia). e mRNA expression levels of EC-enriched DEGs in suicides relative to mean expression levels of controls as expressed in mean ± SE (upper) and dot plot showing gene expression across cell types (lower). f Subcluster of the top-30 genes selected using maximum neighborhood component method from protein–protein interaction (PPI) networks constructed using the 251 DEGs with confidence cut-off of 0.4. g Featured EC-related processes among top-10 gene ontology biological process (GO-BP) terms enriched in DEGs are expressed by p-value and % overlap with the entire gene list of each GO-BP term. Percent overlaps are color-coded as indicated. h Top-5 co-expressed transcription factors (TFs) with DEGs suggested by the ARCHS4 TF co-expression database are expressed by p-value and number of co-expressed genes with each TF. Numbers of co-expressed DEGs are grouped and color-coded as indicated