Using GeneReg to construct time delay gene regulatory networks

The R package GeneReg is based on time delay linear regression, which can generate a model of the expression levels of regulators at a given time point against the expression levels of their target genes at a later time point. There are two parameters in the model, time delay and regulation coefficient. Time delay is the time lag during which expression change of the regulator is transmitted to change in target gene expression. Regulation coefficient expresses the regulation effect: a positive regulation coefficient indicates activation and negative indicates repression. GeneReg was implemented on a real Saccharomyces cerevisiae cell cycle dataset; more than thirty percent of the modeled regulations, based entirely on gene expression files, were found to be consistent with previous discoveries from known databases.GeneReg is an easy-to-use, simple, fast R package for gene regulatory network construction from short time course gene expression data. It may be applied to study time-related biological processes such as cell cycle, cell differentiation, or causal inference.With the rapid development of microarray technology, more and more short time course gene expression data have been generated; with such abundant high-throughput screening data available, researchers have tried to infer, or reverse-engineer, gene networks. In general, the existing models for network inference can be grouped into three categories: logical models, continuous models and single-molecule level models [1]. Logical models such as Boolean networks and Petri nets could represent the network structure but are unable to describe dynamic processes. While single-molecule level models such as stochastic simulation algorithm could provide high resolution modeling and analysis, but only on limited molecules with well-known reactions among them. Single-molecule level models are not suitable for large scale regulatory network reconstruction. There were several widely-used general algorithms for network