Fig. 1

Analysis of the DNA methylation profile associated to trastuzumab resistance in breast cancer cell lines. a Schematic flow chart used to identify differentially methylated genes associated to trastuzumab resistance after comparing the sensitive (SK) and resistant (SKTR) to trastuzumab human breast cancer cell lines. b Scatter plot representing DNA methylation normalized levels (β values) of SK and SKTR cell lines. Red and green triangles indicate the CpGs that gained and lost, respectively, a methylation level ≥ 0.20 in SKTR with respect to SK cells. c Supervised hierarchical clustering of the most variable CpGs (Δβ ≥ 0.20) from island and promoter regions between the SK and SKTR cell lines. d Summary of gene ontology (GO) analysis of the biological process categories for the 152 differentially methylated genes at CpG island and promoter levels between the SK and SKTR cell lines. e Venn diagram showing the differentially methylated and differentially expressed genes (obtained by RNA-Seq) between the SK and SKTR cell lines. The name of the 31 hypermethylated and downregulated genes in SKTR is indicated