Fig. 5

The most influential Parkinson’s disease clinical axis involves genetic pathways associated with neuroinflammation. a Identification of substantia nigra (SN) cell types associated with Parkinson’s disease, Alzheimer’s disease, inflammatory bowel disease and ulcerative colitis. To identify the associations between genetic risk variants of different complex traits and cell types SN, we used the MAGMA gene set analysis (one-sided positive two-sample t-test). The heatmap colours give different degrees of significance * and ** indicate nominally significant p (< 0.05) and q value (Bonferroni correction for the number of cell types tested) respectively. b Microglia-specific pathways associated with the genetic risk of the phenotypic Axis 1, Alzheimer’s disease, inflammatory bowel disease (IBD) and ulcerative colitis. Gene Ontology (GO) enrichment for substantia nigra (SN) microglia protein–protein interaction (PPI) genes modules. We tested the convergence of disease genetic risk at a functional level across SN microglia-cell specific PPI gene modules using MAGMA gene set analysis (one-sided positive two-sample t-test); * and ** indicate nominally significant p-value (< 0.05) and q value (Bonferroni correction for the number of PPI modules tested), respectively. The top representative GO biological process (BP) terms are shown for modules. The size of circles represents -log(p) for GO enrichment with Fisher’s test; colours correspond to different modules