Fig. 3

Differential expression analyses of proteins identified in microglia derived from homeostatic, LPS-induced neuroinflammation and 5xFAD neurodegeneration mouse models. a Volcano plot representation of differentially expressed proteins comparing 5xFAD with untreated WT mouse microglia. The top 15 proteins with increased (red) and decreased (blue) expression are shown. X-axis represents log₂ transformed fold change (5xFAD vs WT) and y-axis represents -log₁₀ transformed p-value from a pairwise two-tailed T test comparing the two groups. b Gene enrichment map summarizing Gene Ontology (GO) terms and WikiPathways enriched in the 5xFAD vs WT differential expression analysis. Enrichment Maps were created in Cytoscape (Enrichment map plugin) Cytoscape using DAVID-formatted GO-Elite pruned Z-Score output tables. Red or Blue colors indicate significant GO terms (Z-score > 1.96) enriched in differentially expressed protein lists in 5xFAD microglia vs. WT microglia (Red: increased, Blue: decreased). Edge connectivity (Jaccard similarity metric) ranges from 0 (light color intensity) to 1 (dark red or blue intensity). Ontology network node colors represent the degree of average log2 fold change for all differentially expressed members of the ontology in the AD-WT networks. Since no overlap of gene symbols occurs between differential expression list-derived up and down sub-networks, respectively red and blue sub-networks were overlaid. Scale AD-CT: bluest (− 0.75) < −> 0 (white) < −> reddest (2.27 log₂Fold change). c Volcano plot representation of differentially expressed proteins comparing LPS-treated WT with untreated WT mouse microglia. The top 15 proteins with increased (red) and decreased (blue) expression are shown. X-axis represents log₂ transformed fold change (LPS-treated WT vs untreated WT) and y-axis represents -log₁₀ transformed p-value from a pairwise two-tailed T test comparing the two groups. d Gene enrichment map summarizing GO analysis of differentially expressed proteins in LPS-treated WT mouse microglia. Gene enrichments were created as described above using significant GO terms enriched in differentially expressed protein lists comparing microglia isolated from LPS-treated WT and untreated WT mice (Red: increased in LPS-treated WT mice; Blue: decreased in LPS-treated WT mice) microglial proteins. Scale LPS-WT/CT: bluest (− 2.21 log2FC) < −> 0 (white) < −> reddest (1.22 log₂ fold change)