Extracting Protein Regulatory Networks with Graphical Models

During the last decade the development of high‐throughput biotechnologies has resulted in the production of exponentially expanding quantities of biological data, such as genomic and proteomic expression data. One fundamental problem in systems biology is to learn the architecture of biochemical pathways and regulatory networks in an inferential way from such postgenomic data. Along with the increasing amount of available data, a lot of novel statistical methods have been developed and proposed in the literature. This article gives a non‐mathematical overview of three widely used reverse engineering methods, namely relevance networks, graphical Gaussian models, and Bayesian networks, whereby the focus is on their relative merits and shortcomings. In addition the reverse engineering results of these graphical methods on cytometric protein data from the RAF‐signalling network are cross‐compared via AUROC scatter plots.