Table 1.

Tags and descriptions of top five most downloaded plugins

Plugin	Functional tags	Description	Total downloads
BiNGO	Enrichment analysis, GO annotation, ontology analysis	Calculates overrepresented functions (GO terms) in the network and displays them as GO directed acyclic graphs	43,641
MCODE	Clustering, graph analysis	Clusters a given network on the basis of vertex weighting by local neighborhood density and outward traversal from a locally dense seed protein to isolate the dense regions	16,260
AgilentLiteratureSearch	Literature mining, network generation	Mines scientific literature to find publications related to search term and to create interaction network based on the search result	15,432
jActiveModules	Integrated analysis, functional module detection, graph analysis	Finds clusters where member nodes show significant changes in expression levels	12,547
MiMIplugin	Online data import, network generation, interaction database	Retrieves interactions associated with input IDs; user can add own annotations to genes, which can be viewed by different users	10,108

The associated tags, description and total number of downloads are listed for each tag. The Supplementary Data file provides a complete list of plugins we tagged along with descriptions. Tags will be updated over time to gradually improve the classification.