Memory functions reveal structural properties of gene regulatory networks
Fig 3
Patterning of the vertebrate neural tube.
(A) Antibody staining of Wild type (WT) mouse stained for three of the main bands in dorso-ventral patterning. (Image provided by Katherine Exelby). (B) Illustration of neural tube patterning: ventral Shh secreted from the notocord and floor plate (termed “Source”) generates patterned domains along the dorso-ventral axis. Each domain is defined by the expression of a characteristic set of genes. (C) GRN that patterns the three most ventral domains of the neural tube. The chosen separation of bulk (purple) and subnetwork (green) in the application of the Zwanzig-Mori projection is also shown. (D) Simulations of steady state pattern along the dorsoventral axis using a set of thermodynamic equations of the form of eqs (1 and 2). These equations were taken—along with appropriate initial conditions of 0 for all species—from [24]. For all plots where x axis represents neural tube position, zero corresponds to the most ventral point. (E) Full bifurcation diagram illustrating the multistable nature of the network. Shown are steady state concentrations of the four molecular species against neural tube position, with unstable steady states marked dashed. Colours in (D, E) identify genes/proteins in the same way as in the labelling of the illustration (B) and of the network nodes in (C). This colour code is used throughout the paper unless otherwise noted.