The workflow of pathway profiling. The tumor samples of three data sets are classified into luminal A, luminal B, triple-negative, and HER2+ subtypes by clinical data and PAM50 classification results. We then perform pathway enrichment analysis for each subtype in each data set individually using the PWEA algorithm. After that we evaluate our method based on its reproducibility, accuracy, and resolution. Finally, we build a small disease/subtype network based on the pathway profiles of each of the four subtypes of breast cancer as well as related diseases.