Fig. 4

Unbiased transcriptomic analysis of PS19 mice homozygous for APOE4 shows predominant immune signature. Brains of paralyzed PS/E4H mice and 9–10-month-old E4H mice were analyzed by RNAseq. Genes (A), cell types (B), astrocyte gene expression profiles (B) and aging/AD-associated profiles (B) differentially regulated in PS/E4H mice relative to E4H mice is shown. p values adjusted for multiple testing; FDR = 0.05. 1-way Anova. qval denotes false discovery rate. The enriched up- and down-regulated genes were plotted onto pathways using the GO database (C) and KEGG pathway database (D) and represented in bubble plots. Pathways with an over-represented p-value ≤ 0.05, the number of module genes within the pathway > 15 and an enrichment score > 1.5 are depicted. The bubble plots are colored by p-value and sized by the enrichment score. Size, number of genes within each module; ES, Enrichment Score; q value, false discovery rate. N = 4 mice for PS/E4H and 3 mice for E4H