ClueGO swMATH ID: 22916 Software Authors: Bindea G, Mlecnik B, Hackl H et al Description: ClueGO is a Cytoscape plug-in that visualizes the non-redundant biological terms for large clusters of genes in a functionally grouped network. The identifiers can be uploaded from a text file or interactively from a network of Cytoscape. The type of identifiers supported can be easily extended by the user. ClueGO performs single cluster analysis and comparison of several clusters (lists of genes). From the ontology sources used, the terms are selected by different filter criteria. The related terms which share similar associated genes can be fused to reduce redundancy. The ClueGO network is created with kappa statistics and reflects the relationships between the terms based on the similarity of their associated genes. On the network, the node colour can be switched between functional groups and clusters distribution. ClueGO charts are underlying the specificity and the common aspects of the biological role. The significance of the terms and groups is automatically calculated. ClueGO is easy updatable with the newest files from Gene Ontology, KEGG, WikiPathways and Reactome. To extend it’s functionality get as well CluePedia. Homepage: http://apps.cytoscape.org/apps/cluego Related Software: STRING; IntAct; KEGG; Cytoscape; gcrma; BioGRID; Bioconductor; R; Reactome; PANTHER; MCODE; iCDI-PseFpt; DrugBank; GPCR-GIA; iEzy-drug; Clustal X; MEGA; InterViewer; NeMoFinder; BiNGO Cited in: 7 Documents Standard Articles 1 Publication describing the Software Year Cluego: a cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks Bindea, Gabriela; Mlecnik, Bernhard; Hackl, Hubert; Charoentong, Pornpimol; Tosolini, Marie; Kirilovsky, Amos; Fridman, Wolf-Herman; Pagès, Franck; Trajanoski, Zlatko; Galon, Jérôme 2009 all top 5 Cited by 20 Authors 1 Delgado, Alberto Santos 1 Fan, Jianqing 1 Ferro, Alfredo 1 Giugno, Rosalba 1 Jatana, Nidhi 1 Ke, Zheng Tracy 1 Keith, Jonathan M. 1 Latha, N. 1 Liu, Han 1 Micale, Giovanni 1 Mohammadnejad, Javad 1 Mongiovì, Misael 1 Ovacik, Ayse Meric 1 Podder, Avijit 1 Pulvirenti, Alfredo 1 Razaghi-Moghadam, Zahra 1 Shafaghati, Leila 1 Shasha, Dennis E. 1 von Stechow, Louise 1 Xia, Lucy all top 5 Cited in 6 Serials 2 Methods in Molecular Biology 1 Mathematical Biosciences 1 Bulletin of Mathematical Biology 1 The Annals of Statistics 1 Data Mining and Knowledge Discovery 1 Journal of Theoretical Biology Cited in 5 Fields 6 Biology and other natural sciences (92-XX) 1 General and overarching topics; collections (00-XX) 1 Combinatorics (05-XX) 1 Statistics (62-XX) 1 Computer science (68-XX) Citations by Year