Mapping connections in signaling networks with ambiguous modularity
Lill D, Rukhlenko OS, Mc Elwee AJ, Kashdan E, Timmer J, Kholodenko BN.
Modular Response Analysis (MRA) is a suite of methods that under certain assumptions permits the precise reconstruction of both the directions and strengths of connections between network modules from network responses to perturbations. Standard MRA assumes that modules are insulated, thereby neglecting the existence of inter-modular protein complexes. Such complexes sequester proteins from different modules and propagate perturbations to the protein abundance of a downstream module retroactively to an upstream module. MRA-based network reconstruction detects retroactive, sequestration-induced connections when an enzyme from one module is substantially sequestered by its substrate that belongs to a different module. Moreover, inferred networks may surprisingly depend on the choice of protein abundances that are experimentally perturbed, and also some inferred connections might be false. Here, we extend MRA by introducing an approach, which allows for a computational restoration of modular insulation, unambiguous network reconstruction and discrimination between solely regulatory and sequestration-induced connections for a range of signaling pathways. Although not universal, our approach significantly extends MRA methods to signaling networks with retroactive interactions between modules arising from substantial enzyme sequestration effects.