On the impact of the distance between two genes on their interaction curve.

We analyze a basic building block of gene regulatory networks using a stochastic/geometric model in search of a mathematical backing for the discrete modeling frameworks. We consider a network consisting only of two interacting genes: a source gene and a target gene. The target gene is activated by the proteins encoded by the source gene. The interaction is therefore mediated by activator proteins that travel, like a signal, from the source to the target. We calculate the production curve of the target proteins in response to a constant-rate production of activator proteins. The latter has a sigmoidal shape (like a simple delay line) that is sharper and taller when the two genes are closer to each other. This provides further support for the use of discrete models in the analysis gene regulatory networks. Moreover, it suggests an evolutionary pressure towards making the interacting genes closer to each other to make their interactions more efficient and more reliable.