Figure 3

Four case studies are represented using one or several of the major visualization methods applied in oncogenomics. (a) Heatmap of oncogenomic alterations ordered by mutual exclusivity plotted with Gitools. In the upper half of the image, colors indicate the type of alteration: mutations (green), CNA gain (red) and CNA loss (blue). The heatmap below shows expression data (high expression in red and low expression in green) for the same samples and genes, allowing the visual observation that genomics regions whose copy number is amplified tend to have higher expression values. (b) The same data as in (a), with the same color code for alterations, represented as a network of functional interactions between the genes, extracted from the cBio Cancer Genomics Portal. The halo around the four selected nodes is divided into three sectors. Changes in the proportion of samples with altered copy number are indicated in red (gain) or blue (loss) in the top sector, whereas changes in the proportion of samples with mutations are indicated in green in the lower-right sector. Expression changes are shown in light red (increase) and light blue (decrease) in the lower-left sector of the halo. Panels (c-e) include clinical information. Each tumor sample is assigned to one of four subtypes of glioblastoma, color-coded as dark green (classical), light green (mesenchymal), orange (neural) and red (proneural). (c) Heatmap of pathway expression levels plotted with Gitools. Each column is a tumor sample. The subtype is represented in colors in the top row and each row represents a biological pathway. The color of each cell indicates the Zscore of the sample level enrichment analysis (SLEA) of the pathway in the sample. Clear differences in the expression values in different pathways can be observed for different cell subtypes. (d) Same data as in (c) represented in the form of a network, drawn using CircleMap. Each node is a pathway and its edges indicate functional interactions between pathways as extracted from KEGG. The two halos around each node indicate the Zscore of the pathway in each sample and the clinical subtype. (e) CNA and expression data for the EGFR gene region of glioblastoma samples as shown by IGV. The top part of the plot indicates the genomic position we are observing. Each sample is shown as a horizontal track, ordered by clinical subtype. Within each clinical subtype, the tracks in the upper half illustrate CNA whereas those below show expression. This visualization reveals clear differences in the CNA and expression of the EGFR locus in different clinical subtypes. (f) Adaptations of Circos plots of three breast tumors with three very different alteration landscapes. The four circles in each plot, from outermost inwards, represent the human chromosomes, mutations, copy number alterations, and structural rearrangement.