Reverse Engineering of Gene Networks with LASSO and Nonlinear Basis Functions

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Abstract
The quest to determine cause from effect is often referred to as reverse engineering in the context of cellular networks. Here we propose and evaluate an algorithm for reverse engineering a gene regulatory network from time‐series and steady‐state data. Our algorithmic pipeline, which is rather standard in its parts but not in its integrative composition, combines ordinary differential equations, parameter estimations by least angle regression, and cross‐validation procedures for determining the in‐degrees and selection of nonlinear transfer functions. The result of the algorithm is a complete directed network, in which each edge has been assigned a score from a bootstrap procedure. To evaluate the performance, we submitted the outcome of the algorithm to the reverse engineering assessment competition DREAM2, where we used the data corresponding to the InSilico1 and InSilico2 networks as input. Our algorithm outperformed all other algorithms when inferring one of the directed gene‐to‐gene networks.