Table 1.

Basic concepts of biological networks.

Structure assessment	Definition	Utility	References
Degree distribution	Distribution of probabilities of degrees in a specific network.	Comparisons, scale-free networks. Clear indicator of the presence of hubs when it is combined with the centrality measurement. Degree provides clues about modules in a network by determining the number of interactions shared between neighboring nodes.	Képès, 2007
Shortest path	The shortest path between two nodes in a biological network.	Connectivity.	Perumal et al., 2009
Average diameter	The minimum number of edges connecting any two nodes over all possible pairs.	Information flow, Small World. Capacity and time of the response of a system, so that in networks with a high centrality, signaling processes are favored.	Képès, 2007
Node clustering coefficient	The ratio of connections to neighboring nodes to the number of all possible connections.	Comparisons, scale-free, hierarchical.	Képès, 2007
Betweenness—centrality	The ratio of the number of k-shortest paths passing through a node and its nearest neighbor links.	Identifies hubs (highly connected nodes in a network), important in pathogenicity and potential target for drugs. Hubs may potentially disconnect the network if they are removed or blocked.	Goh et al., 2001; Perumal et al., 2009
Assortativity	The probability of connection of a node with others of the same degree.	Robustness to node deletion.	Newman, 2010

Summary of structural measurements of the topology of a network and their utility in a biological context.