A method of generating a dynamic pathway map (DPM) is provided. The method includes accessing a model database that stores a probabilistic pathway model that comprises a plurality of pathway elements, a first number of the plurality of pathway elements are cross-correlated and assigned an influence level for at least one pathway on the basis of known attributes, a second number of the plurality of pathway elements are cross-correlated and assigned an influence level for at least one pathway on the basis of assumed attributes. The method includes measuring a patient sample to identify measured attributes of the patient sample and using a plurality of the measured attributes of the patient sample, via an analysis engine, to modify the probabilistic pathway model to obtain the DPM, wherein the DPM has reference pathway activity information for a particular pathway, the reference pathway indicating deviations from the probabilistic pathway model.