A Bayes Regularized Ordinary Differential Equation Model for the Inference of Gene Regulatory Networks

Abstract

Differential equation models provide a detailed, quantitative description of transcription regulatory networks. However, due to the large number of model parameters, they are usually applicable to small networks only, with at most a few dozen genes. Moreover, they are not well suited to deal with noisy data. In this chapter, we show how to circumvent these limitations by integrating an ordinary differential equation model into a stochastic framework. The resulting model is then embedded into a Bayesian learning approach. We integrate the-biologically motivated-expectation of sparse connectivity in the network into the inference process using a specifically defined prior distribution on model parameters. The approach is evaluated on simulated data and a dataset of the transcriptional network governing the yeast cell cycle.