Abstract
The existence of discrete phenotypic traits suggests that the complex regulatory processes which produce them are functionally modular. These processes are usually represented by networks. Only modular networks can be partitioned into intelligible subcircuits able to evolve relatively independently. Traditionally, functional modularity is approximated by detection of modularity in network structure. However, the correlation between structure and function is loose. Many regulatory networks exhibit modular behaviour without structural modularity. Here we partition an experimentally tractable regulatory network-the gap gene system of dipteran insects-using an alternative approach. We show that this system, although not structurally modular, is composed of dynamical modules driving different aspects of whole-network behaviour. All these subcircuits share the same regulatory structure, but differ in components and sensitivity to regulatory interactions. Some subcircuits are in a state of criticality, while others are not, which explains the observed differential evolvability of the various expression features in the system.
Highlights
Systems biology aims to understand the function and evolution of complex regulatory networks
Modularity The gap gene system is composed of three dynamical modules
The analysis asks which of the four trunk gap genes are required—or, more accurately, which ones are not—to drive correct expression dynamics in nuclei at different positions along the antero-posterior (A–P) axis during cleavage cycle 14A (C14A)
Summary
Systems biology aims to understand the function and evolution of complex regulatory networks. This requires some sort of hierarchical decomposition of these networks into manageable and intelligible subsystems, whose properties and behaviour can be analysed and understood in relative isolation (Simon, 1962; Riedl, 1975; Lewontin, 1978; Bonner, 1988; Raff, 1996; West-Eberhard, 2003; Schlosser and Wagner, 2004; Callebaut et al, 2005). The most common strategy to identify functional modules is to partition the graph representing a network into simple motifs (Shen-Orr et al, 2002; Alon, 2007) or subcircuits
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