DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures

 

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dc.contributor.author Mazandu, Gaston en_ZA
dc.contributor.author Mulder, Nicola en_ZA
dc.date.accessioned 2015-11-23T11:44:12Z
dc.date.available 2015-11-23T11:44:12Z
dc.date.issued 2013 en_ZA
dc.identifier.citation Mazandu, G. K., & Mulder, N. J. (2013). DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures. BMC bioinformatics, 14(1), 284. en_ZA
dc.identifier.uri http://hdl.handle.net/11427/15243
dc.identifier.uri http://dx.doi.org/10.1186/1471-2105-14-284
dc.description.abstract BACKGROUND: The use of Gene Ontology (GO) data in protein analyses have largely contributed to the improved outcomes of these analyses. Several GO semantic similarity measures have been proposed in recent years and provide tools that allow the integration of biological knowledge embedded in the GO structure into different biological analyses. There is a need for a unified tool that provides the scientific community with the opportunity to explore these different GO similarity measure approaches and their biological applications. RESULTS: We have developed DaGO-Fun, an online tool available at http://web.cbio.uct.ac.za/ITGOM, which incorporates many different GO similarity measures for exploring, analyzing and comparing GO terms and proteins within the context of GO. It uses GO data and UniProt proteins with their GO annotations as provided by the Gene Ontology Annotation (GOA) project to precompute GO term information content (IC), enabling rapid response to user queries. CONCLUSIONS: The DaGO-Fun online tool presents the advantage of integrating all the relevant IC-based GO similarity measures, including topology- and annotation-based approaches to facilitate effective exploration of these measures, thus enabling users to choose the most relevant approach for their application. Furthermore, this tool includes several biological applications related to GO semantic similarity scores, including the retrieval of genes based on their GO annotations, the clustering of functionally related genes within a set, and term enrichment analysis. en_ZA
dc.language.iso eng en_ZA
dc.publisher BioMed Central Ltd en_ZA
dc.rights This is an Open Access article distributed under the terms of the Creative Commons Attribution License en_ZA
dc.rights.uri http://creativecommons.org/licenses/by/2.0 en_ZA
dc.source BMC Bioinformatics en_ZA
dc.source.uri http://www.biomedcentral.com/bmcbioinformatics/ en_ZA
dc.subject.other Ontology (GO) data en_ZA
dc.subject.other protein analyses en_ZA
dc.subject.other DaGO-Fun en_ZA
dc.title DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures en_ZA
dc.type Journal Article en_ZA
dc.rights.holder 2013 Mazandu and Mulder; licensee BioMed Central Ltd. en_ZA
uct.type.publication Research en_ZA
uct.type.resource Article en_ZA
dc.publisher.institution University of Cape Town
dc.publisher.faculty Faculty of Health Sciences en_ZA
dc.publisher.department Institute of Infectious Disease and Molecular Medicine en_ZA
uct.type.filetype Text
uct.type.filetype Image


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This is an Open Access article distributed under the terms of the Creative Commons Attribution License Except where otherwise noted, this item's license is described as This is an Open Access article distributed under the terms of the Creative Commons Attribution License