Figure 3

Functional annotation of AD risk genes. (A) KEGG pathways and (B) GO terms of biological processes enrichment of AD risk genes. In (B), each dot represents a significantly enriched GO term, whose –log₁₀(P-value) and AD risk gene count are indicated by the color and size of the dot, respectively. (C) Expression of AD risk genes in different tissues. Three expression clusters are indicated by the black boxes. See Supplementary Fig. S3 for details. (D) Cell type enrichment analysis. We analyzed the expression of AD risk genes in different types of single cells from frontal and visual cortices, cerebellum, and adult brain. The red dashed line represents FDR = 0.05, and cell types whose transcriptomes were significantly enriched with the expression of AD risk genes are shown, with their brain regions indicated. Used cell type abbreviations: Ast, astrocytes; End, endothelial; Ex, excitatory; Gran, granule; In, inhibitory; Mic, microglia; Neu, neuron; Oil, oligodendrocytes; OPC, oligodendrocytes precursor; Per, pericytes; Purk, purkinje. (E) Network connectivity of AD risk genes in the co-expression network of both AD patients and normal controls in the brain region BM22. Each dot represents an AD risk gene. The gray dashed line marks the threshold for network hub genes either in the co-expression network of AD patients or normal controls. Blue and green dots represent network hub genes only in the co-expression network of AD patients and only in the co-expression network of normal controls, respectively. See Supplementary Fig. S6 for details and other brain regions.