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ClueGO is a Cytoscape App that visualizes non-redundant biological terms for large clusters of genes/proteins in a functionally grouped network.
Besides human and mouse data, more than 200 other organisms are available for download. Identifiers can be uploaded from a text file or interactively from a network of Cytoscape. ClueGO performs single cluster analysis and comparison of several clusters/lists. Terms and pathways are selected from multiple ontology sources using different filter criteria. The ClueGO network is created with kappa statistics and reflects the relationships between terms based on the similarity of their associated genes. The multiple visualization styles of the network can be switched to show functional groups, distribution of clusters and significance. ClueGO charts are underlying the specific and the common biological roles of analyzed clusters. The significance of terms and groups is automatically calculated. Related terms which share similar associated genes can be fused to reduce the redundancy. ClueGO can be automatically updated with the newest files from Gene Ontology, KEGG, WikiPathways and Reactome. To extend it's functionality get as well CluePedia.
ClueGO visualizes as functionally grouped networks terms and pathways resulted from other enrichment analyses.
Cytoscape Automation enables scientific workflows written in many languages through the CyREST. ClueGO functions are now REST enabled, and allow the integration of ClueGO in analytical pipelines.

Bindea G*, Mlecnik B*, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pages F, Trajanoski Z and Galon J. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology annotation networks. Bioinformatics 2009.25(8):1091-1093

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