Fig 1. Network topology and molecular logic.
The left panel shows a schematic diagram of the network topology, reproduced from Dunn et al. [16]. Each node corresponds to a given gene and their placement from left to right is chosen to indicate a trend of downstreamness from three external inputs. In our mechanistic model, each gene produces a unique transcription factor at a rate which depending on the binding state of its promoter site. These transcription factors then go on to bind and activate (black arrow) or repress (red bar) other genes. The three nodes on left correspond to extra-cellular signals, which are either absent or present. The right panel shows our assumed molecular logic of transcriptional regulation when there are N = 2 promoter sites per gene. Each circle is a binding site: it can be either empty (white), bound by an activator (green), or bound by a repressor (red). The right panel lists possible combinations of the promoter sites. Depending on the configuration of the promoter site, transcription factors are produced with rates 0, Ωαm, and Ωαmax, modeling the effects of cooperative binding.