BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks

By Steven Maere, Karel Heymans, Martin Kuiper. Bioinform., 2005

4,189 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/5598922da04bdb14c8ff7c52738ca47194493532

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In Molecular Biology

Citations in the corpus

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists (2009, neutral): “A large repertoire of tools for enrichment analysis has been developed in recent years, including GoMiner [3], FatiGO [4], BiNGO [5], GOAT [6], DAVID [7] and others.”
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists (2007, background): “A number of publicly available bioinformatics tools have addressed the first three points above, including, but not limited to, GoMiner, DAVID, EASE, GOstat, Onto-express, GoToolBox, FatiGO, GOSSIP, GFINDer, GOBar, and so on [1-25].”
Enriching the gene set analysis of genome-wide data by incorporating directionality of gene expression and combining statistical hypotheses and methods (2013, methodology): “These methods are popular among GO-based tools (6), including BiNGO (7), DAVID (8), GOstat (9) and GOEAST (10).”
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources (2020, methodology): “, all analytes measured, or all analytes in a pathway database) used for each pathway [205,206].”
Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes (2012, methodology): “…transcriptome, proteome, and metabolome data are displayed for the nt clusters, examples of gene connections in selected pathways based on own as networks, with constituents marked as assessed from proteome data, alysis results from Cytoscape (Smoot et al., 2011) BiNGO (Maere et al., 2005) uded.”
Application of BACarray for comparative analysis of CNS cell types (2008, methodology): “Gene Ontologies was performed with the BiNGO plugin for the cytoscape software (Maere et al., 2005).”
GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis (2008, background): “Among the few available GO analysis tools with graphical output (12,19,20,23,28), only EasyGO has similar functions, but it is limited to several plants and farm animals (28).”
Visualizing GO Annotations. (2016, methodology): “Of note, there are Cytoscape plugins specialized for handling groups of GO terms: EnrichmentMap (11) and BINGO (12).”
clusterMaker: a multi-algorithm clustering plugin for Cytoscape (2011, methodology): “, using DAVID [41] or BiNGO [42]), another powerful analytical approach is to examine clusters for corresponding molecular interactions.”
Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica) (2010, methodology): “Of 179 identified targets in our rice degradome library (except for 3 TAS3 transcripts), 105 transcripts have Gene Ontology (GO) annotations (Maere et al., 2005) and they are obviously enriched in transcription factor and transcription regulatory activity (Supplemental Fig.”
The human urinary proteome contains more than 1500 proteins, including a large proportion of membrane proteins (2006, methodology): “Characterization of the urinary proteome via Gene Ontology annotation The identified proteins were functionally categorized based on universal Gene Ontology (GO) annotation terms [31] using the Biological Networks Gene Ontology (BiNGO) program package [32,33].”