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Fig. 4 | Journal of Neuroinflammation

Fig. 4

From: Comparative analysis of transcriptome remodeling in plaque-associated and plaque-distant microglia during amyloid-β pathology progression in mice

Fig. 4

Microglial gene expression remodeling between plaques-associated and plaques-distant AD microglia. A Heatmap of differentially expressed genes in PAM (violet) versus PCM (orange) along aging. The scaled expression value (row Z score) is shown in a blue–red color scheme with red indicating higher expression, and blue lower expression. The full data are available in Additional file 20: Table S8A. B Boxplots of Eigengene values for each sample in the most abundant WGCNA module of PAM versus PCM DEGs (497 genes). Statistical analyses: 2-ways ANOVA with Microglia subtype and Age as between subjects’ factors. Subtype p < 0.001; Subtype:Age p < 0.05. FDR corrected post hoc tests; ***p < 0.001. C Cytoscape representation of deregulated GO terms (“Biological Process” category) in the most abundant module of PAM versus PCM DEGs (497 genes). The full data are available in Table S8B. D Venn diagram showing the overlap between DEGs in PAM versus CM (FDR < 0.05, violet circle), PCM versus CM (FDR < 0.05, orange circle), and PAM versus PCM (FDR < 0.05, green circle). (E) Bar plot showing the significance (− log10(p-value)) of enrichment of AD GWAS genes in PAM and PCM DEGs. Different AD GWAS sets corresponding to different p-value cutoffs (Marioni al., 2018), were tested. The numbers under brackets indicate the number of ortholog genes at the cutoff, and the numbers in columns, the numbers of PAM or PCM DEG GWAS genes

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