Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation

The data-driven inference of intracellular networks is one of the key challenges of computational and systems biology. As suggested by recent works, a simple yet effective approach for reconstructing regulatory networks comprises the following two steps. First, the observed effects induced by directed perturbations are collected in a signed and directed perturbation graph (PG). In a second step, Transitive Reduction (TR) is used to identify and eliminate those edges in the PG that can be explained by paths and are therefore likely to reflect indirect effects.