Fig. 2: Genome-wide microarray analysis identified a list of genes that were differentially expressed by Aβ42 and their altered expression was reversed by Lpc-EV.

a, b A hypothetical RROH map with up- or downregulated genes by Aβ42 or Lpc-EV (a). A hypergeometric map between the genes changed by Aβ42 (x-axis) and those by Lpc-EV (y-axis). The genes were ranked based on expression differences between two comparison groups by their log₁₀-transformed t-test p values and plotted on the x- and y-axes (b). Quadrants A and D contained 11,003 and 9,479 transcripts, respectively. The top 20% of transcripts ranked on expression differences were selected and used for further analyses. Up and down arrows indicate upregulated and downregulated expression, respectively. c, d Serial K-means clustering of the selected genes and subsequent Gene Ontology (GO) enrichment analyses led to identify seven functional clusters (c), which were visualized by a combined PPI network (d). Clusters 6 and 7 contained functional groups of genes for neurotrophic factors (Cluster 6) and for transcription and epigenetic regulation (Cluster 7). e, h A summary of key features of Clusters 6 (e, g) and 7 (f, h). Top three functional groups assigned by GO terms in Cluster 6 (e) and the PPI of 75 genes assigned with a GO term for “neurogenesis” (g). Top three functional groups covered by GO terms in Cluster 7 (f) and the PPI of 98 genes assigned with a GO term for “regulation of transcription, DNA-templated” (h).