Comparisons of changes in expression between brain regions showed regional differences in Ache, Apoe, Ptk2b, Sorl1, and Sort1. Thus, both AD pathology and the absence of microglia have minimal effects on AD-related genes, and importantly, we observe no alterations in gene expression or protein production in the absence of microglia that could account for reduced plaque formation. Here, SORL1 is linked to Alzheimer disease.