A framework enabling dissection of the effects of motif structure (feedback or feedforward), nature of the controller (mRNA or protein), and regulation mode (transcriptional, post-transcriptional or translational) on the response to a step change in the input is presented. We have used a common model for gene expression and a common parameter set. Both structures have an activating input and repressing regulatory effect. The effect of global parameter variation on steady-state gain, overshoot, peak time, and peak duration was studied. Protein mediated motifs showed higher degree of adaptation. RNA mediated motifs had a lower tendency to exhibit peaks. For both motif structures, overshoot correlated negatively with peak time. Peak duration is a concave function of peak time for all motifs.