GOToolBox: functional analysis of gene datasets based on Gene Ontology

By David Martin, C. Brun, É. Remy, Pierre Mouren, D. Thieffry, Bernard Jacq. Genome Biology, 2004

388 citations recorded by the source corpus.

We have developed methods and tools based on the Gene Ontology (GO) resource allowing the identification of statistically over- or under-represented terms in a gene dataset; the clustering of functionally related genes within a set; and the retrieval of genes sharing annotations with a query gene. GO annotations can also be constrained to a slim hierarchy or a given level of the ontology. The source codes are available upon request, and distributed under the GPL license.

View Paper: https://www.semanticscholar.org/paper/924a6bbe31c4c774d1dd66a4320e2f054dce9315

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Citations in the corpus

• In silico prediction of protein-protein interactions in human macrophages (2001, methodology): “GO-proxy : this program is part of the GOToolBox suite [45].”
• 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].”
• Semantic Similarity in Biomedical Ontologies (2009, methodology): “GOToolBox also implements some set similarity techniques applied to GO graphs, namely Czekanowski-Dice and Jaccard [32].”
• Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists (2008, unknown): “Interestingly, biological module/ classes of annotation terms, provided by PalS (67), DAVID (61) and GoToolBox (18), present heterogeneous annotation terms or genes in a group scope.”
• Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges (2012, methodology): “es/GOToolBox/) [10]”
• Enrichment or depletion of a GO category within a class of genes: which test? (2007, background): “Thus, it is not justified to claim, as Masseroli et al. (2004) do, that ‘the x and Fisher’s exact tests have less power than the hypergeometric and binomial distribution tests’.”
• Systematic mapping of occluded genes by cell fusion reveals prevalence and stability of cis-mediated silencing in somatic cells (2014, background): “Gene ontology (GO) analysis (Martin et al. 2004) showed that occluded genes in 129TF are highly enriched for regulatory functions, and include many key factors controlling important cellular and developmental processes as well as members of essentially every major signaling and transcription factor ”
• KOBAS server: a web-based platform for automated annotation and pathway identification (2006, methodology): “A variety of web-based tools have been developed for GO-based analysis, including Gotcha (2), GoFigure (3), FatiGO (4), GFINDer (5), GOstat (6), NetAffx (7), GOToolBox (8) and Onto-Tools (9).”
• TreeDyn: towards dynamic graphics and annotations for analyses of trees (2006, methodology): “spreadsheets) or by using specific online tools such as GOToolbox [18].”