Limitations of a gene expression network constructed from late-stage postmortem human Alzheimer’s disease brain tissue are 1) the presence of co-pathologies, which do not allow one to differentiate between changes that are a specific consequence of pathological forms of tau, amyloid β, or other events such as vascular damage and 2) the inability to determine how co-expression networks change as the disease progresses. The gene discussed is MAPT; the disease is early-onset autosomal dominant Alzheimer disease.