ClueGO

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.


References in zbMATH (referenced in 9 articles , 1 standard article )

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  1. Micale, Giovanni; Giugno, Rosalba; Ferro, Alfredo; Mongiovì, Misael; Shasha, Dennis; Pulvirenti, Alfredo: Fast analytical methods for finding significant labeled graph motifs (2018)
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  3. Keith, Jonathan M. (ed.): Bioinformatics. Volume I. Data, sequence analysis, and evolution (2017)
  4. Shafaghati, Leila; Razaghi-Moghadam, Zahra; Mohammadnejad, Javad: A systems biology approach to understanding alcoholic liver disease molecular mechanism: the development of static and dynamic models (2017)
  5. Fan, Jianqing; Ke, Zheng Tracy; Liu, Han; Xia, Lucy: QUADRO: a supervised dimension reduction method via Rayleigh quotient optimization (2015)
  6. Ovacik, Ayse Meric: Network biology in development of monoclonal antibody therapeutics (2015)
  7. Podder, Avijit; Jatana, Nidhi; Latha, N.: Human dopamine receptors interaction network (DRIN): a systems biology perspective on topology, stability and functionality of the network (2014)
  8. Doderer, Mark; Yoon, Kihoon; Robbins, Kay A.: SIDEKICK: genomic data driven analysis and decision-making framework (2010) ioport
  9. Bindea, Gabriela; Mlecnik, Bernhard; Hackl, Hubert; Charoentong, Pornpimol; Tosolini, Marie; Kirilovsky, Amos; Fridman, Wolf-Herman; Pagès, Franck; Trajanoski, Zlatko; Galon, Jérôme: Cluego: a cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks (2009) ioport