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

ABSTRACT:

Background

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.

Results

In this work we introduce novel variants for PG generation and TR, leading to significantly improved performances. The key modifications concern: (i) use of novel statistical criteria for deriving a h

SUBMITTER: Pinna A 

PROVIDER: S-EPMC4231426 | biostudies-literature | 2013 Aug

REPOSITORIES: biostudies-literature