DNA-mRNA plot illustrating copy number induced gene expression changes for TOB1. Copy number and gene expression data in 32 breast cancer patients was integrated, and the effect of copy number changes on mRNA expression levels was evaluated using a permutation-based non-parametric test as described in the third case study of this article. The tool "Plot copy number induced gene expression" was then used to illustrate the results for the TOB1 gene (Transducer of ErbB2 1). In the plot each patient is depicted as a blue circle, whose radius is proportional to the probability of the copy number call, and whose centerpoint indicates the gene expression level. The filled red circles have a radius proportional to the estimated expected call probabilities, and their centerpoint indicate the estimated mean expression for the respective call.