Abstract: A system and method of predicting the course of progression of a disease and determining a personalized therapeutic regime for treating the disease in a subject includes obtaining the subject's normal-tissue transcriptome. The normal-tissue transcriptome is statistically correlated with the subject's perturbed transcriptome to identify one or more deregulated mechanisms; and statistics derived from the identified deregulated mechanism are used to predict the course of progression of the disease and to a recommend a personalized therapeutic regime for treating the disease. The perturbed transcriptome may in some cases be determined from a cancer of the subject, and in other cases from viral infected tissue cultured from the subject.