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BiNGO is a tool to determine which Gene Ontology (GO) categories are statistically overrepresented in a set of genes or a subgraph of a biological network. BiNGO maps the predominant functional themes of a given gene set on the GO hierarchy, and outputs this mapping as a Cytoscape graph. Gene sets can either be selected or computed from a Cytoscape network (as subgraphs) or compiled from sources other than Cytoscape (e.g. a list of genes that are significantly upregulated in a microarray experiment). The main advantage of BiNGO over other GO tools is the fact that it can be used directly and interactively on molecular interaction graphs. Another plus is that BiNGO takes full advantage of Cytoscape's versatile visualization environment. This allows you to produce customized high-quality figures. Features include : 1. Assessing over-representation or under-representation of GO categories 2. Graph or gene list input 3. batch mode: analyze several clusters simultaneously using same settings 4. Different GO and GOSlim ontologies 5. Wide range of organisms 6. Evidence code filtering 7. Hypergeometric or binomial test for over-representation 8. Multiple testing correction using Bonferroni (FWER) or Benjamini&Hochberg (FDR) correction 9. Interactive visualization of results mapped on the GO hierarchy 10. Extensive results in tab-delimited text file format 11. Make and use custom annotations, ontologies and reference sets 12. Open source **If you use BiNGO in your research, please cite:** *Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in biological networks. **Bioinformatics** 21, 3448-3449.* [http://www.ncbi.nlm.nih.gov/pubmed/15972284 (PubMed)]