Reverse engineering gene regulatory networks by modular response analysis – a benchmark

Abstract

Gene regulatory networks control the cellular phenotype by changing the RNA and protein composition. Despite its importance, the gene regulatory network in higher organisms is only partly mapped out. Here, we investigate the potential of reverse engineering methods to unravel the structure of these networks. Particularly, we focus on modular response analysis (MRA), a method that can disentangle networks from perturbation data. We benchmark a version of MRA that was previously successfully applied to reconstruct a signalling-driven genetic network, termed MLMSMRA, to test cases mimicking various aspects of gene regulatory networks. We then investigate the performance in comparison with other MRA realisations and related methods. The benchmark shows that MRA has the potential to predict functional interactions, but also shows that successful application of MRA is restricted to small sparse networks and to data with a low signal-to-noise ratio.