Figure 3

Volcano plot of results from the linear model analysis of renal cell carcinoma. Differential gene expression between cancer and normal samples was analyzed using linear modelling as described in the first case study of this article. The results were visualized using the interactive volcano plot of Chipster, so that the relative gene expression between cancer and normal samples was plotted on the x-axis, and the -log 10 -transformed p-values from the linear model were plotted on the y-axis. Each dot denotes one gene (probeset). The colored dots are statistically significantly (p < = 0.05) down-regulated (green) or up-regulated (red) genes. Users can select genes by drawing a box around them and create new gene lists based on these selections.