In case of inhibitor experiments (Protein kinase inhibitors for the dissection of signal transduction pathways), how do we explain the fact when an inhibitor itself produces some changes (either up-regulation or down-regulation) different from the basal level/control.
for example, if a experiment consists of 4 groups- control C, treatment T, inhibitor I, inhibitor + treatment I+T, and if the inhibitor itself in this case produces changes different from the control, how do we explain this observation?

The cells most likely have a basal level of the protein which is inhibited. Check that first .....