Table 2.

Examples of popular and useful network support applications

Application	Network function addressed
Network Analyzer	Calculates an extensive array of network topological parameters to facilitate identification of nodes of interest and relevant network structural characteristics
MCODE	Detects and prioritizes highly interconnected regions within a network
jActive Modules	Identifies expression activated subnetworks, connected network regions that exhibit significant changes in expression
ReOrient Plugin	Facilitates visual comparison of adjacent networks by locating common nodes in the same relative location
BiNGO	Determines GO category statistical over- or under-representation from a set of genes/proteins within a network or subnetwork of interest, visualized as a GO hierarchy network to map significant themes by biological process, cellular component, or molecular function
Enrichment Map	Visualizes networks of gene set enrichment analysis results, where nodes represent gene sets and edges their mutual overlap (rather than connecting nodes by nested GO classification, as done in BiNGO), clustering highly redundant gene sets to improve enrichment analysis navigation and interpretation
NCBI Entrez Gene User Interface/NCBI Client	Imports gene/protein interactions, annotations, and attributes from NCBI Entrez Gene for network derivation
Agilent Literature Search	Queries multiple text-based search engines to obviate the need for manual search and extraction of gene/protein interactions for network generation