Fig. 2

Example workflow of BRCA-Pathway. There are several ways to select KEGG pathways. In this example, pathway selection by DEG is described. First, select subpopulation by breast cancer subtype and clinical features (a). If patients with ‘Basal-like’ subtype are selected, then pathways including differentially expressed genes are listed as the result of computation of Wilcoxon rank-sum test (b). Select pathways from the list then BRCA-Pathway visualizes multi-omics data of patients whose subtype is ‘Basal-like’. Users can view the pathway by three different data types. Gene expression, mutation, and CNV data are visualized in separate way or integrated way. Genes having specific omics-pattern are highlighted by selecting the omics condition. For example, genes having no mutation and of which CNV is loss or del but overexpressed are selected for highlighting then the pathway turns shaded except the highlighted genes (c)