APOE and Alzheimer disease: Modules that correlated in a positive direction with ApoE were characterized by the top GO terms “threonine-type peptidase activity,” “L-serine metabolic process,” and “regulation of inflammatory response.” Those that correlated in a negative direction with ApoE were “acute phase response,” “postsynaptic membrane,” “translation,” “synaptic transmission,” and “mitochondrion.” We compared each AD ApoE variant to control E3/E3 to assess which modules contained the most differentially abundant proteins between disease and control for each variant (Figure 2C).