Evaluate disease correlations by using pathway profiles. (A) Pathway profiles for luminal A, luminal B, HER2+, and triple-negative subtypes of breast cancer, as well as ovarian cancer, glioblastoma multiforme (GBM), and obesity. Each red rectangle represents an enriched pathway. From right to left, KEGG pathways are sorted according to pathway categories and have the same order as the FDR values of enriched pathways in these 7 diseases/subtypes (Additional file 6). Due to limitation of space, here only pathway categories are labeled. This figure roughly shows that luminal A and luminal B subtypes are closer to the HER2+ subtype than the triple-negative subtype. (B) Disease/subtype correlation networks based on pathway profile. Each node represents one disease and subtypes are embedded in a metanode representing breast cancer [72–74]. The width of each edge is roughly proportional to the correlation between the disease/subtype pair. Here only the significant correlations (p-value < 0.05) are displayed (See Additional file 7). The network is drawn by the VisANT system [67–71].