Biological pathways underlying region-specific microglial ageing. (a) Transcript-to-transcript correlation network graph of transcripts differentially expressed according to age (p < 0.05 with FDR correction) and clustered using a Markov clustering algorithm. Nodes represent individual transcripts and edges the degree of correlation in expression pattern between them. Colours denote discrete clusters. Circled region includes clusters with greater expression in cerebellum and/or increasing with age; square region includes clusters with greater expression in forebrain regions and/or declining expression with age. (b) Cluster position and mean expression profile of transcripts from cluster 2 indicating greater and/or earlier age-related changes. (c, d) Interferon pathway genes showing (c) earlier and/or (d) greater/selective increases in expression in cerebellar microglia compared to forebrain regions during ageing. Data show mean ± SD, n = 4 independent samples, each pooled from tissue from eight mice. *p < 0.05, **p < 0.01, ***p < 0.001 vs 4 month; #p < 0.05, ##p < 0.01, ###p < 0.001 vs 12 month, two-way ANOVA with Bonferroni correction. (e) Heat maps showing microarray expression patterns of selected immunoreceptor family genes during ageing arranged according to activating (A) or inhibitory (I) classification. Row Z-score intensities represent the mean of four independent samples per region and age with red indicating higher expression and lower expression in blue. (f) Expression patterns of Cd300 family genes show interaction between brain region and age for activating but not inhibitory members. Data show mean ± SD, n = 4 independent samples, each pooled from tissue from eight mice. *p < 0.05, **p < 0.01, ***p < 0.001 vs 4 month; #p < 0.05, ##p < 0.01, ###p < 0.001 vs 12 month, two-way ANOVA with Bonferroni correction. (g, h) Cluster position and mean expression profile of transcripts from cluster 14 indicating selective decline in expression during ageing in hippocampal microglia. (h) Expression profiles of selected genes from cluster 14. Data show mean ± SD, n = 4 independent samples, each pooled from tissue from eight mice. *p < 0.05, **p < 0.01, ***p < 0.001 vs 4 month; #p < 0.05, ##p < 0.01, ###p < 0.001 vs 12 month, two-way ANOVA with Bonferroni correction. Str, striatum; Hpp, hippocampus; Ctx, cerebral cortex; Cbm, cerebellum. Specific p values for all statistical comparisons are presented in .