Fig. 3

TCGA BRCA multi-omics data exploration with BRCA-Pathway. Visualization of TCGA BRCA with BRCA-Pathway (a) Multi-omics data of patients whose subtypes are ‘Basal-like’ is mapped on hsa04110 (Cell cycle). Users can view pathway maps in three different data types. Gene expression, mutation and CNV data are visualized either separately or integrated. Genes with specific patterns are highlighted by selecting the conditions. For example, genes, having no mutation and of which CNV is loss or del but that are over-expressed, are selected. Genes in the pathway except the highlighted genes become shaded (b) Clicking a gene entry on the pathway displays multi-omics data of the gene such as gene expression level compared with normal sample pool and with tumor sample pool, mutation count and ratio, CNV as -2 (del), -1 (loss), 0 (neutral), 1 (gain), 2 (amp) with the count of patients having each CNV value and Pearson correlation coefficients of TF-TG gene expression. Three columns represent the correlation of TF-TG in normal sample pool, tumor sample pool and selected subpopulations pool, respectively. Correlation with p-value over 0.05 are shaded. c Selecting genes, Oncoprint shows copy number variation (amp or del) and mutation in the mutual exclusive way between selected genes. In this case, some extremely over-expressed genes (fold change>10 by normal sample pool) and RB1 are selected and the figure shows mutual exclusive pattern between CCNE2, RB1, CCNE1 and CDKN2A (top 4 rows respectively)