Fig. 3

Differentially expressed genes (DEGs) are over-represented in pathways associated with Alzheimer’s disease (AD). Over-representation analysis (ORA) showing the 8 DEGs in Fig. 2 were over-represented in molecular and biological pathways thought to be linked to AD including TGF-β signaling, serine hydrolase activity, and histone modification. Auto-annotation descriptions of the 3 major clusters displayed corresponded with the pathways that were most significantly over-represented by the DEGs. Overrepresentation analysis significance was determined utilizing the Benjamini–Hochberg FDR multiple testing correction method by applying a significance threshold of 0.05. The pathways analyzed were obtained from readily available online databases including Gene Ontology (GO) pathways describing molecular function, cellular components, and biological processes; biological pathway databases including KEGG, Reactome, and WikiPathways; and the Human Phenotype Ontology database. Cytoscape applications were utilized to produce the displayed network map that organizes and automatically generates networks of overlapping gene sets that infer interactions between the identified pathways [37, 38]