An integrated genomic analysis to clarify drug resistance in MCF7-ADR (drug-resistant breast cancer cell line). (A) Schematic representation of an integrated genomic analysis. During the acquisition of drug resistance in breast cancer cell (MCF7; parental cell line and MCF7-ADR; drug resistance cell line), a large number of genomic alterations were raised, such as amplification or deletion, to modulate the expression of genes and miRNAs. Based on aCGH, miRNAs and genes on the aberration region of genome are selected for further analysis of its target genes and their associated-pathways in silico. (B) aCGH analysis of MCF7 and MCF7-ADR as compared with normal human female genome. Blue line shows normal vs. MCF7, and red line shows normal vs. MCF7-ADR (top). Amplified or deleted genome regions (fold change > 3) are highlighted (bottom). (C) The numbers of genes and miRNAs located on the amplified or deleted genome regions (FC > 3). (D and E) The expression tendency of genes located on the aberrant genome regions. 426 genes from MCF7 amplified regions and 6 genes from MCF7-ADR amplified regions are plotted in left panels of each scatter plot. Six genes from MCF7 deleted regions and 25 genes from MCF7-ADR deleted regions are plotted in right panels of each scatter plot.