BiNGO

BiNGO: A Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. Summary: The Biological Networks Gene Ontology tool (BiNGO) is an open-source Java tool to determine which Gene Ontology (GO) terms are significantly overrepresented in a set of genes. BiNGO can be used either on a list of genes, pasted as text, or interactively on subgraphs of biological networks visualized in Cytoscape. BiNGO maps the predominant functional themes of the tested gene set on the GO hierarchy, and takes advantage of Cytoscape’s versatile visualization environment to produce an intuitive and customizable visual representation of the results. Availability: http://www.psb.ugent.be/cbd/papers/BiNGO/


References in zbMATH (referenced in 13 articles )

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  1. Sanguinetti, Guido (ed.); Huynh-Thu, Vân Anh (ed.): Gene regulatory networks. Methods and protocols (2019)
  2. Micale, Giovanni; Giugno, Rosalba; Ferro, Alfredo; Mongiovì, Misael; Shasha, Dennis; Pulvirenti, Alfredo: Fast analytical methods for finding significant labeled graph motifs (2018)
  3. Álvarez-Miranda, Eduardo; Farhan, Hesso; Luipersbeck, Martin; Sinnl, Markus: A bi-objective network design approach for discovering functional modules linking Golgi apparatus fragmentation and neuronal death (2017)
  4. Kasabov, Nikola (ed.): Springer handbook of bio-/neuro-informatics (2014)
  5. Bruckskotten, Marc; Looso, Mario; Cemic, Franz; Konzer, Anne; Hemberger, Jurgen; Kruger, Markus; Braun, Thomas: PCA2GO: a new multivariate statistics based method to identify highly expressed GO-terms (2010) ioport
  6. Jupiter, Daniel; Şahutoğlu, Jessica; Vanburen, Vincent: TreeHugger: a new test for enrichment of gene ontology terms (2010)
  7. Ren, Xianwen; Zhang, Xiang-Sun: A linear programming model based on network flow for pathway inference (2010)
  8. Sikora, Marek; Gruca, Aleksandra: Quality improvement of rule-based gene group descriptions using information about GO terms importance occurring in premises of determined rules (2010)
  9. Tchagang, Alain B.; Gawronski, Alexander; Bérubé, Hugo; Phan, Sieu; Famili, Fazel; Pan, Youlian: GOAL: A software tool for assessing biological significance of genes groups (2010) ioport
  10. Eden, Eran; Navon, Roy; Steinfeld, Israel; Lipson, Doron; Yakhini, Zohar: \textitgorilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists (2009) ioport
  11. Mao, Linyong; Van Hemert, John L.; Dash, Sudhansu; Dickerson, Julie A.: \textitarabidopsisgeneco-expression network and its functional modules (2009) ioport
  12. Ricardo Vencio, Ilya Shmulevich: ProbCD: enrichment analysis accounting for categorization uncertainty (2007) arXiv
  13. Vêncio, Ricardo Zn; Shmulevich, Ilya: Probcd: Enrichment analysis accounting for categorization uncertainty (2007) ioport