Fig. 4

Microarray and methylation analysis. a) Microarray analysis from parental and PDX-resistant cells. Hierarchical cluster analysis of gene expression profiles indicated the 72 genes with commonly expression changes (more than 2-fold or less than 0.5-fold) between the PDX-resistance cell lines. The scale shows the level of expression, where red indicates increased gene expression, green indicates decreased expression, and the intensity of color correlated to the magnitude change. b) Gene set enrichment analysis. Significantly enriched gene signatures in GSEA analysis with microarray analysis from parental and PDX-resistant cells using the hallmark gene set. NOM; nominal, FDR; false discovery rate. c) DNA methylation heatmap showing unsupervised clustering of the top 5% most variable genes among PDX-resistant cell. d) The boxplot indicates the distribution of mean differences of beta values between of the CpG islands, shore, open sea, TSS 200 and 1st exon