Fig. 2

Integration of copy-number, gene expression and single nucleotide variants. a Box plot representations showing focal copy number variations identified by SNP array on X-axis and gene expression quantified by RNA sequencing on Y-axis. Focally amplified or deleted genes from all four cell lines showed a positive trend with over expression or under expression respectively. b Scatter plot representation of genes harboring single nucleotide variants and it’s expression from all four cell lines. Variants identified by whole exome sequencing are displayed by genomic coordinates on X-axis and normalized quantity of gene expression (by transcriptome sequencing) is displayed on Y-axis. Red line denotes 0.01 log10(FPKM + 1) filter which removes ~50 % of the total variants