APOE and Autoimmunity: We also identified a cluster (cluster 7), which included 125 genes that were upregulated by microglia in response to chronic stimuli, such as neurodegeneration and autoimmunity, but were unchanged or decreased in microglia responding to acute LPS-induced endotoxemia; these genes were termed "chronic response genes" and included genes such as Apoe, Clec7a, Gas6, Itgax and Siglecf (Fig. 7b, Additional file 1: Fig. S9e-f, Additional 1: Table S3).