De novo reconstruction of gene regulatory networks from time series data, an approach based on formal methods

Reverse engineering of gene regulatory relationships from genomics data is a crucial task to dissect the complex underlying regulatory mechanism occurring in a cell. From a computational point of view the reconstruction of gene regulatory networks is an undetermined problem as the large number of possible solutions is typically high in contrast to the number of available independent data points. Many possible solutions can fit the available data, explaining the data equally well, but only one of them can be the biologically true solution. Several strategies have been proposed in literature to reduce the search space and/or extend the amount of independent information. In this paper we propose a novel algorithm based on formal methods, mathematically rigorous techniques widely adopted in engineering to specify and verify complex software and hardware systems. Starting with a formal specification of gene regulatory hypotheses we are able to mathematically prove whether a time course experiment belongs or not to the formal specification, determining in fact whether a gene regulation exists or not. The method is able to detect both direction and sign (inhibition/activation) of regulations whereas most of literature methods are limited to undirected and/or unsigned relationships. We empirically evaluated the approach on experimental and synthetic datasets in terms of precision and recall. In most cases we observed high levels of accuracy outperforming the current state of art, despite the computational cost increases exponentially with the size of the network. We made available the tool implementing the algorithm at the following url: http://www.bioinformatics.unisannio.it.