Figure 2

Boxplots of two SNPs, rs3088324 and rs11966226, showing significant association with copy number variation. (A-B) Boxplots were used to demonstrate the difference in copy number between the specific SNPs (AG versus GG for rs3088324 and CC versus CT for rs11966226). Significance level was determined by a Wilcoxon rank sum test. The Y-axis represents copy number. (A) KDM5B, rs3088324, was correlated with copy number amplifications. (B) RNF217, rs11966226, was correlated with copy number deletions. (C-D) To evaluate whether CNVs were able to drive downstream gene expression changes, a Wilcoxon rank sum test was performed on the expression difference between tumor and normal tissue for each SNP. The two genes, (C) KDM5B and (D) RNF217, both showed significantly differential expression (p-values < 0.05) and concordance in terms of the direction of change of CNVs and gene expression. The Y-axis denotes relative expression ratios on a log scale. Dotted lines indicate the unchanging baseline.