Estimating dynamic models for gene regulation networks

MOTIVATION Transcription regulation is a fundamental process in biology, and it is important to model the dynamic behavior of gene regulation networks. Many approaches have been proposed to specify the network structure. However, finding the network connectivity is not sufficient to understand the network dynamics. Instead, one needs to model the regulation reactions, usually with a set of ordinary differential equations (ODEs). Because some of the parameters involved in these ODEs are unknown, their values need to be inferred from the observed data. RESULTS In this article, we introduce the generalized profiling method to estimate ODE parameters in a gene regulation network from microarray gene expression data which can be rather noisy. Because numerically solving ODEs is computationally expensive, we apply the penalized smoothing technique, a fast and stable computational method to approximate ODE solutions. The ODE solutions with our parameter estimates fit the data well. A goodness-of-fit test of dynamic models is developed to identify gene regulation networks.