ArticlePloS one2014
Information content-based Gene Ontology functional similarity measures: which one to use for a given biological data type?
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Gene Duplication and Gain in the Trematode Atriophallophorus winterbourni Contributes to Adaptation to Parasitism.Genome biology and evolution · 2021Article
- Graph embeddings on gene ontology annotations for protein-protein interaction prediction.BMC bioinformatics · 2020Article
- Statistical Approach for Biologically Relevant Gene Selection from High-Throughput Gene Expression Data.Entropy (Basel, Switzerland) · 2020Article
- Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance.Scientific reports · 2020Article
- UFO: A tool for unifying biomedical ontology-based semantic similarity calculation, enrichment analysis and visualization.PloS one · 2020Article
- GO2Vec: transforming GO terms and proteins to vector representations via graph embeddings.BMC genomics · 2019Article
- STarFish: A Stacked Ensemble Target Fishing Approach and its Application to Natural Products.Journal of chemical information and modeling · 2019Article
- GO functional similarity clustering depends on similarity measure, clustering method, and annotation completeness.BMC bioinformatics · 2019Article
- Word and Sentence Embedding Tools to Measure Semantic Similarity of Gene Ontology Terms by Their Definitions.Journal of computational biology : a journal of computational molecular cell biology · 2019Article
- Gene Ontology Enrichment Improves Performances of Functional Similarity of Genes.Scientific reports · 2018Article
- CommWalker: correctly evaluating modules in molecular networks in light of annotation bias.Bioinformatics (Oxford, England) · 2018Article
- A new method for evaluating the impacts of semantic similarity measures on the annotation of gene sets.PloS one · 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
- The effects of shared information on semantic calculations in the gene ontology.Computational and structural biotechnology journal · 2017Article
- Similarities between plant traits based on their connection to underlying gene functions.PloS one · 2017Article
- A-DaGO-Fun: an adaptable Gene Ontology semantic similarity-based functional analysis tool.Bioinformatics (Oxford, England) · 2016Article
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Abstract
The current increase in Gene Ontology (GO) annotations of proteins in the existing genome databases and their use in different analyses have fostered the improvement of several biomedical and biological applications. To integrate this functional data into different analyses, several protein functional similarity measures based on GO term information content (IC) have been proposed and evaluated, especially in the context of annotation-based measures. In the case of topology-based measures, each approach was set with a specific functional similarity measure depending on its conception and applications for which it was designed. However, it is not clear whether a specific functional similarity measure associated with a given approach is the most appropriate, given a biological data set or an application, i.e., achieving the best performance compared to other functional similarity measures for the biological application under consideration. We show that, in general, a specific functional similarity measure often used with a given term IC or term semantic similarity approach is not always the best for different biological data and applications. We have conducted a performance evaluation of a number of different functional similarity measures using different types of biological data in order to infer the best functional similarity measure for each different term IC and semantic similarity approach. The comparisons of different protein functional similarity measures should help researchers choose the most appropriate measure for the biological application under consideration.
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