Gene clustering trees and TOM plots that visualize interconnectivity patterns often suggest the presence of large modules. Network theory offers a wealth of intuitive network concepts for describing the pairwise relationships among genes that are depicted in cluster trees and heat maps [11]. To illustrate this point, we describe two network concepts in the following. By visual inspection of Figures 2C and 4B, genes appear to be highly interconnected, e.g. turquoise module genes form a reddish square in the TOM plot. This property of dense connections among the genes of module q can be measured using the concept of module density, which is defined as the average adjacency of the module genes:
