ArticleBMC bioinformatics2013
DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures.
Article in BMC bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Study on the semi-supervised learning-based patient similarity from heterogeneous electronic medical records.BMC medical informatics and decision making · 2021Trial
- From Macro to Micro: De Novo Genomes of Aedes Mosquitoes Enable Comparative Genomics Among Close and Distant Relatives.Genome biology and evolution · 2025Article
- HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey.BMC bioinformatics · 2022Article
- Meta-path Based Prioritization of Functional Drug Actions with Multi-Level Biological Networks.Scientific reports · 2019Article
- Post genome-wide association analysis: dissecting computational pathway/network-based approaches.Briefings in bioinformatics · 2019Review
- Hydroxyurea-Induced miRNA Expression in Sickle Cell Disease Patients in Africa.Frontiers in genetics · 2019Article
- From homogeneous to heterogeneous network alignment via colored graphlets.Scientific reports · 2018Article
- Gene Ontology Enrichment Improves Performances of Functional Similarity of Genes.Scientific reports · 2018Article
- A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1.BMC plant biology · 2017Article
- CTLA-4-mediated posttranslational modifications direct cytotoxic T-lymphocyte differentiation.Cell death and differentiation · 2017Article
- Protein complex finding and ranking: An application to Alzheimer's disease.Journal of biosciences · 2017Article
- Exploring Approaches for Detecting Protein Functional Similarity within an Orthology-based Framework.Scientific reports · 2017Article
- Whole-genome resequencing of honeybee drones to detect genomic selection in a population managed for royal jelly.Scientific reports · 2016Article
- A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool.Bioinformatics (Oxford, England) · 2016Article
- The post-genomic era of biological network alignment.EURASIP journal on bioinformatics & systems biology · 2015Article
- Categorizer: a tool to categorize genes into user-defined biological groups based on semantic similarity.BMC genomics · 2014Article
- Using biological networks to improve our understanding of infectious diseases.Computational and structural biotechnology journal · 2014Review
- Information content-based Gene Ontology functional similarity measures: which one to use for a given biological data type?PloS one · 2014Article
- The use of semantic similarity measures for optimally integrating heterogeneous Gene Ontology data from large scale annotation pipelines.Frontiers in genetics · 2014Article
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2 authors.
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Abstract
backgroundThe 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.
resultsWe 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.
conclusionsThe 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.
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