Finally, to complete our assessment of PHENSIM capabilities, we run several simulations to perform 4 case studies on known biological experiments: (i) anti-cancer effects of metformin, (ii) Everolimus (RAD001) treatment in breast cancer, (iii) effects of exosomal vesicles on hematopoietic stem/progenitor cells (HSPCs) in the bone marrow (BM) and (iv) testing TNFα/siTPL2-dependent synthetic lethality on a subset of human cancer cell lines. This evidence concerns the gene TNF and breast cancer.