CSEA revealed the pathways characteristics of the integral genomic signature predicting Trastuzumab-based treatment responses, such as the MTORC1 signaling predicting sensitive response, a major downstream effector of HER2 signaling, and the ER and EMT pathways predicting resistant response, both of which are known to endow HER2 therapy and chemotherapy resistance in breast cancer. Here, ESR1 is linked to breast carcinoma.