Predicting dynamic signaling network response under unseen perturbations

“…First, construction of the CSN relied solely on gene expression profile data, and future work to integrate somatic mutation information, epigenetic status [ 26 , 27 ], and pathways could potentially improve the performance of our network models. Furthermore, some other dynamic and direct features, such as time-course gene expression [ 28 ] or protein signaling [ 29 ], might better illustrate a cell line and potentially give a more reliable CSN. Second, construction of the DSN used the 1-D and 2-D structural features of each drug, which might provide too many features for small molecule drugs, and yet ignored the 3-D structure features which may be important for certain drugs.…”