In summary, two different pathway scoring algorithms (PSA and GSA) identified the overlapped up-regulated transcriptomic pathways enriched in neurodegeneration disease association (AD causal risk pathway/disease association), neuroinflammation (activated microglia/cytokines), and others (autophagy/neuronal cytoskeleton/angiogenesis/myelination), caused by the human APP transgene. Here, APP is linked to Alzheimer disease.