beMφs and microglia maintain unique predicted functions in multiple experimental models. (A) Selected beMφ Gene Ontology biological functions that are identified as enriched by GSVA in the Cx3cr1^CreER/+::Csf1r^Flox/Flox model with head-covered BMT and tamoxifen treatment, traditional BMT, and BMT/PLX5622 when compared with the microglia in the same experiment. The boxplots show the distribution of the −log10(FDR-adjusted p-value) of the corresponding functional term calculated for each of the three experiments. A complete list of functions commonly up-regulated in beMφs versus microglia in all datasets can be found in Table S2. (B) Selected microglia Gene Ontology biological functions that are identified as enriched by GSVA in the Cx3cr1^CreER/+::Csf1r^Flox/Flox model with head-covered BMT and tamoxifen treatment, traditional BMT, and BMT/PLX5622 when compared with beMφs in the same experiment. Boxplots show the distribution with mean of the −log10(FDR-adjusted p-value) of the corresponding functional term calculated for each of the three experiments. A complete list of functions commonly up-regulated in microglia versus beMφs in all datasets can be found in Table S2.