Generating synthetic gene regulatory networks

Abstract

Reconstructing GRN from microarray dataset is a very challenging problem as these datasets typically have large number of genes and less number of samples. Moreover, the reconstruction task becomes further complicated as there are no suitable synthetic datasets available for validation and evaluation of GRN reconstruction techniques. Synthetic datasets allow validating new techniques and approaches since the underlying mechanisms of the GRNs, generated from these datasets, are completely known. In this paper, we present an approach for synthetically generating gene networks using causal relationships. The synthetic networks can have varying topologies such as small world, random, scale free, or hierarchical topologies based on the well-defined GRN properties. These artificial but realistic GRN networks provide a simulation environment similar to a real-life laboratory microarray experiment. These networks also provide a mechanism for studying the robustness of reconstruction methods to individual and combination of parametric changes such as topology, noise (background and experimental noise) and time delays. Studies involving complicated interactions such as feedback loops, oscillations, bi-stability, dynamic behavior, vertex in-degree changes and number of samples can also be carried out by the proposed synthetic GRN networks. © 2008 Springer Berlin Heidelberg.