Analyzing molecular reaction networks: from pathways to chemical organizations.

Pathways are typically the central concept in the analysis of biochemical reaction networks. A pathway can be interpreted as a chain of enzymatical reactions performing a specific biological function. A common way to study metabolic networks are minimal pathways that can operate at steady state called elementary modes. The theory of chemical organizations has recently been used to decompose biochemical networks into algebraically closed and self-maintaining subnetworks termed organizations. The aim of this paper is to elucidate the relation between these two concepts. Whereas elementary modes represent the boundaries of the potential behavior of the network, organizations define metabolite compositions that are likely to be present in biological feasible situations. Hence, steady state organizations consist of combinations of elementary modes. On the other hand, it is possible to assign a unique (and possibly empty) set of organizations to each elementary mode, indicating the metabolites accompanying the active pathway in a feasible steady state.