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Table 2 Centralities calculated by the CentiScaPe Cytoscape’s plugin

From: From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data

Centrality

Description

Biological meaning

Diametera

Defines the longest shortest path in the network

 

Average distancea

Defines the mean length of all the shortest paths in the network

 

Degreeb

Describes the number of neighbors a node has

Highlights the number of nodes that regulated/regulate the node v

Eccentricityb

Describes the longest shortest paths a node develop, giving us a proximity information

Highlights the easiness of a protein to reach/to be reached by all the other proteins in the network

Closenessb

Describes, for the node v, the minimal sum of all the distances in the network

Highlights the probability of a protein to be functionally relevant for several proteins, but irrelevant for a few others

Radialityb

Describes the integration of a node into the network

Highlights the ability of a protein to be functionally relevant for several proteins, but irrelevant for a few others

Centroidb

Describes the neighborhood of nodes by highlighting nodes that have the highest number of neighbors separated by the minimal shortest path

Highlights a protein that tends to be functionally capable of organizing discrete protein clusters or modules

Stressb

Describes the number of shortest paths that pass through a node

Highlights the relevance of a protein as functionally capable of holding together communicating nodes

Betweennessb

Describes, for each couple of nodes, the number of shortest paths that pass through a specific node

Highlights the relevance of a protein as functionally capable of holding together communicating nodes

Bridgingb

Describes the neighborhood of nodes by highlighting nodes with a high number of high-degree neighbors

Highlights a protein possibly bringing in communication sets of regulatory protein

Eigenvectorb

Describes a sort of weighted degree, where not only the number of the neighbors is important but also the Eigenvector of the neighbors itself

Highlights a protein interacting with several important proteins, suggesting a central super-regulatory role or a critical target of a regulatory pathways

Edge betweennessc

Describes, for each couple of nodes, the shortest paths that pass through a specific edge

Highlights the relevance of the interaction as capable of organizing regulatory process

  1. For each centrality, it is described the topological and biological meaning. The a indicates network’s properties. The b indicates node’s properties. The c indicates edge’s property