Depression-associated pairs spanned Notch (JAG1-NOTCH2, DLL1-NOTCH3, DLL4-NOTCH3), ephrin (EFNA5-EPHA5, EFNA5-EPHA7, EFNA5-EPHA4), and extracellular matrix pathways (SLIT1-ROBO1, NTN1-DCC). Here, NOTCH3 is linked to major depressive disorder.