### Table 1.Network terms and characteristics used in this chapter.

Network TermDefinition
Definitions taken from references 11, 28 and 40
Node Represents a gene (generally protein or RNA)
Edge Represents the interaction between nodes. Edges are graphically displayed by lines connecting nodes. Different experimental conditions can be displayed either by a number on the edge or by edge colour
Hub A node that has many connections to other nodes
Undirected This term can apply to an edge or the entire network. It implies that nodes interact but not regulation or direction
Directed This term can apply to an edge or the entire network. It implies direction to the connection between nodes (e.g., regulation)
Scale-Free network Network characterised by a power law degree distribution. I.e. there are a small number of highly connected hubs and the probability of these hubs is statistically more significant than in a random network
Random network Each pair of nodes is connected with a probability (p). Node degrees follow a Poisson distribution where most nodes have about the same number of links
Hierarchical network A type of scale free network allowing for hubs but also for modular sub-networks within the entire network
Degree (k) The number of neighbours of a node. Describes connectiveness
Clustering coefficient (C) The average ratio of the proportion of edges between connected nodes and the possible number of edges between them (i.e., the number of connections if the graph is fully connected), values between 0 and 1. 1 being fully connected and 0 being fully unconnected.
Assortativity The average degree of the nearest neighbours of a node. A negative
(NC) correlation indicates that hubs tend to interact with nodes with a low degree. A positive correlation suggests a modular mode with hubs linking to other hubs
Shortest path (SP) The shortest path between each two nodes (i.e., the number of edges connecting two nodes)
Betweenness (B) The frequency with which a node is located on the shortest path between all other nodes. Nodes with a high betweenness control the flow of information across the network
Proteomic seed A protein significantly differentially expressed between conditions as identified by proteomic screening
Network crosstalk The degree of network proximity and connectivity between (groups of) proteins, modelled as the amount of information flow between these proteins n a PPI network
Sub-graph or Graphlets A small sub-motif of a network occurring more than would be expected by random
RGF Distance Identifes all subgraphs with 3-5 nodes in two networks and compares the frequency of their appearance
GGDA statistic Calculates node specific permutation groups (called automorphism orbits) within each of the 29 (2-5 nodes) possible subgraphs of the two networks being compared