The pathway enrichment analysis revealed that the top co-expressed genes were enriched for pathways involving antigen processing and presentation, prion disease, and the complement system in microglia (Fig. 6d), while APOE-associated pathways in astrocytes included protein processing in the endoplasmic reticulum, and antigen processing and presentation (Fig. 6c), again suggesting both recurrent and cell-type-specific processes mediated by distinct APOE molecular partners. Here, APOE is linked to prion disease.