Identifying dynamical modules from genetic regulatory systems: applications to the segment polarity network

Abstract

Background: It is widely accepted that genetic regulatory systems are 'modular', in that the whole system is made up of smaller 'subsystems' corresponding to specific biological functions. Most attempts to identify modules in genetic regulatory systems have relied on the topology of the underlying network. However, it is the temporal activity (dynamics) of genes and proteins that corresponds to biological functions, and hence it is dynamics that we focus on here for identifying subsystems.

Evolution of Networks for Body Plan Patterning; Interplay of Modularity, Robustness and Evolvability

“…Furthermore, our findings demonstrate the importance of considering functional aspects of biologically relevant network modularity [36]–[39].…”

“…However, it is recently being suggested that functional or dynamic rather than architectural network modularity may be most relevant for network functioning and evolution [36]–[40]. Note that architectural and functional modularity do not necessarily overlap.…”

Dynamics of actively regulated gene networks

“…This definition of a module in terms of dynamics and function is probably the most common. One way of disclosing modules in this sense as dynamic elements related to the attractors (point-like or periodic) of a (discrete time) network is given in [34].…”

Drivers of structural features in gene regulatory networks: From biophysical constraints to biological function

“…Such motifs thus provide a signature of the underlying phenotypic constraints. In some cases the motifs on their own lead to clear insights into the regulatory logic used, while in other cases it is necessary to consider the motifs in a larger context [196], for instance by taking into account interactions with adjacent motifs.…”