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Table 1 Glossary

From: Network analysis identifies protein clusters of functional importance in juvenile idiopathic arthritis

Term Definitiona
Bottleneck A network position that limits the performance of the system. Described by the mathematical idea of betweeness centrality - a description of the number of paths travelling through a node in a network. An example would be a rate-limiting enzymatic reaction.
Cluster A measure of the tendency of network nodes to form groups. It manifests from a high density of edges between nodes. In biological networks a cluster could represent a protein complex.
Connectivity/degree The number of connections (see edge) made by any node within a network.
Edge An interaction between two nodes. Commonly represents a protein:protein interaction but can also be representative of other biological phenomena such as co-expression.
Interactome A network representing a whole set of direct and/or indirect interactions related to a specific biological phenomenon.
Minimal Essential Network (MEN) Top 10% of network protein nodes, as scored by connectivity and bottleneck network properties. Corresponds to highly functionally related positions within the network.
Network analysis Analysis that relates the structural and mathematical properties of a network to its function.
Node A vertex within a network. In biological networks a node will usually be a gene, protein or metabolite.
Seed genes A starting set of genes or metabolites of interest that are used to generate an interactome model by inferring joining interactions algorithmically.
  1. aFurther technical references are given in Stevens et al., [33].