By representing viSNE results in 3D (Additional file 8: Figure S4, Additional file 9), we observed that homeostatic microglia may reach AD-associated states (Magenta or Yellow modules) via at least 3 distinct pathways (Additional file 8: Figure S4, Additional file 9) including a pro-inflammatory pathway (lower band) comprising of LPS-upregulated modules, a second potentially anti-inflammatory pathway (middle band) containing LPS-downregulated/IL4-upregualted modules and a third possible pathway of microglial activation (upper band). This evidence concerns the gene IL4 and Alzheimer disease.