Figure 4

Schematic representation of intracellular information processing. The transcriptional-regulatory (TR) network is composed of input TFs (not regulated by other TFs) (squares), intermediate TFs (regulated by at least one other TF) (circles) and output nodes (regulated effector genes) (triangles). Signals external to the cell can affect the input- and at least some of the intermediate TFs directly or indirectly through signaling cascades. Internal signals, through the activity of the overall molecular interaction network of the cell (shaded in grey) can potentially affect all nodes of the TR network through allosteric regulation, posttranslational modification, etc. Within the TR network the various signals are integrated within relatively distinct subnetworks, or organizers (brown-shaded boxes) composed of intermediate TFs. The TFs within organizers are densely linked but there are only sparse links with TFs in other organizers. A given elementary signal (e.g., Signal X) may affect only a single origon [13], depicted here as the filled symbols, but complex signals may affect several origons simultaneously. As transcription is the 'slow' component of the overall regulatory network in which each link adds a time delay in the regulation, there is a very rich possibility of dynamics carried out on the topology. In particular, nodes might be activated at several time steps (represented by the different fill patterns) corresponding to the propagation of subsequent reaction waves in chemical/interaction space [46].