3.Model Reconciliation. Integrate the observed mRNA and protein
responses with the current, pathway-specific model and
with the global network of protein-protein,
protein-DNA, and other known physical interactions.
4.
4.Model
verification/expansion. Formulate new hypotheses to explain
observations not predicted by the model. Design
additional perturbation experiments to test these and
iteratively repeat steps (2), (3), and (4).