Fig. 4

Global gene expression analysis of APOE ε4-expressing AD patient iNs during amyloid-seeding stage. a Venn diagram showing the overlap of differentially expressed genes between patient iNs expressing APOE ε4 from the amyloid-seeding stage and after the amyloid-seeding stage. The number of 1.5-fold upregulated (top) and 1.5-fold downregulated (bottom) genes are displayed on the Venn diagram. Top: P-value < 5.124e-136. Bottom: P-value < 2.960e-112. b Gene ontology analysis of the differentially expressed genes between APOE ε4-expressing AD patient iNs compared with that of AD patient iNs. c Heatmap showing microarray expression of differentially expressed genes in APOE ε4-expressing AD patient iNs at the amyloid-seeding stage or the amyloid progressive stage. d Scatter plot of the microarray data between APOE ε4-expressing patient iNs at the amyloid-seeding stage and APOE ε4-expressing AD patient iNs after the amyloid-seeding stage. e Scatterplot illustrating the concordance for 9 gene-expression values measured by microarray (x axis) and real-time qPCR (y axis) under each condition. f Gene set enrichment analysis of the microarray data from APOE ε4-expressing AD patient iNs at the amyloid-seeding stage and APOE ε4-expressing AD patient iNs after amyloid-seeding stage. g Graph of the IGFBP3 protein interaction network related to AD risk factors, which is subnetworked by containing direct interaction with proteins encoded by up-regulated overlapping genes (IGFBP5, CLU, IL6, CD44, IRS2) and down-regulated overlapping genes (COL1A2, NFKBIA) in APOE ε4-expressing AD patient iNs at the amyloid-seeding stage