One of the the current challenge for cell biology is understanding of the system level cellular behavior from the knowledge of a network of the individual sub-cellular agents. We address a question of how the model selection affects the predicted dynamic behavior of a gene network. In particular, for a fixed network structure, we compare protein-only models with models in which each transcriptional activation is represented both by mRNA and protein concentrations. We compare linear behavior near equilibria for both cyclic feedback systems and a general system. We show that, in general, explicit inclusion of the mRNA in the model weakens the stability of equilibria. We also study numerically dynamics of a particular gene network and show significant differences in global dynamics between the two types of models.