Sixty-eight a priori gene sets shared enrichment in M turquoise and M yellow, with genes predominantly involved in the ‘neuronal system’ and neurotransmission, neurodegenerative disorders (Huntington’s, Parkinson’s and Alzheimer’s), protein metabolism, DNA repair and replication, transcription and mRNA processing, cell cycling, oxidative phosphorylation, glucose metabolism, mitochondrial function, and MAPK cell signaling pathways. Both M turquoise and M yellow were negatively correlated with AD, suggesting decreased activity/function of these pathways and processes. The full list of shared enriched gene sets between the neuronal modules is available in S4 Table. Shared a priori gene set enrichment between the glial cell-associated modules was predominantly between M green, M pink and M salmon, totaling 18 gene sets, with genes involved in cytokine/immune signaling, cell surface interactions, and cell signaling pathways (JAK/STAT, RhoA and TGF-β), which were upregulated in AD cases. The full list of shared enriched gene sets between the glial enriched modules is available in S4 Table.
