Fig. 2

The graphical user interface and output of ZDOG. a. The interface window, where the user can select which mutation types and datasets available in either COSMIC or TCGA are used for analysis (left). The loaded pathway will be annotated with mutations and displayed. Mutated genes are colored red, blue or grey depending on whether they are oncogenes, tumor-suppressors or neither. Unmutated genes are not colored. By clicking the “calculate dominator tree” button, the user can examine the extent to which mutations in a gene will affect downstream protein components and signaling processes in the pathway under the dominator tree model. b. Dominator tree for the PI3K/Akt signaling pathway, with CSF1 chosen as root. The genes are colored in terms of their mutation frequencies in the COSMIC breast cancer dataset. Protein complexes are represented by a box. Four additional dark arrows are used to highlight the key genes discussed in the case study