1.4 Reconstruction of Biological Networks
In this section, we describe some existing approaches to reconstruct directed and undirected biological networks from gene expression data and gene sets. To reconstruct directed networks from gene expression data, we present Boolean network, probabilistic Boolean network, and Bayesian network models. We discuss cGraph, frequency method and NICO approaches for network reconstruction using gene sets (Fig 1.4). Next, we present relevance networks and graphical Gaussian models for the reconstruction of undirected biological networks from gene expression data (Fig 1.5). The review of models in case of directed and undirected networks is largely based on Refs. [6–8,17–20] and [2,3,13,32], respectively.