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Open Access Highly Accessed Software

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

Gaston K Mazandu and Nicola J Mulder

Author Affiliations

Computational Biology Group, Department of Clinical Laboratory Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Medical School, Observatory, Cape Town, 7925, South Africa

BMC Bioinformatics 2013, 14:284  doi:10.1186/1471-2105-14-284

Published: 25 September 2013

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 webcite, 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.