Generic flux coupling analysis

Arne C. Reimers, Yaron Goldstein, Alexander Bockmayr
2015 Mathematical Biosciences  
Flux coupling analysis (FCA) has become a useful tool for aiding metabolic reconstructions and guiding genetic manipulations. Originally, it was introduced for constraint-based models of metabolic networks that are based on the steady-state assumption. Recently, we have shown that the steady-state assumption can be replaced by a weaker lattice-theoretic property related to the supports of metabolic fluxes. In this paper, we further extend our approach and develop an efficient algorithm for
more » ... ic flux coupling analysis that works with any kind of qualitative pathway model. We illustrate our method by thermodynamic flux coupling analysis (tFCA), which allows studying steady-state metabolic models with loop-law thermodynamic constraints. These models do not satisfy the lattice-theoretic properties required in our previous work. For a selection of genome-scale metabolic network reconstructions, we discuss both theoretically and practically, how thermodynamic constraints strengthen the coupling results that can be obtained with classical FCA. A prototype implementation of tFCA is available at • s is directionally coupled to r, written s → r, if for all v ∈ C, v s = 0 implies v r = 0. Equivalently, we could require that for all v ∈ C, http://dx.
doi:10.1016/j.mbs.2015.01.003 pmid:25619608 fatcat:cngylawv7zbcrkjfajo3hljfk4