ArticleBMC bioinformatics2016
TopoICSim: a new semantic similarity measure based on gene ontology.
Article in BMC bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed.
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- Coherent pathway enrichment estimation by modeling inter-pathway dependencies using regularized regression.Bioinformatics (Oxford, England) · 2023Article
- HiG2Vec: hierarchical representations of Gene Ontology and genes in the Poincaré ball.Bioinformatics (Oxford, England) · 2021Article
- Mantis: flexible and consensus-driven genome annotation.GigaScience · 2021Article
- A Collection of Benchmark Data Sets for Knowledge Graph-based Similarity in the Biomedical Domain.Database : the journal of biological databases and curation · 2020Article
- Handling Big Data Scalability in Biological Domain Using Parallel and Distributed Processing: A Case of Three Biological Semantic Similarity Measures.BioMed research international · 2019Article
- Measures of co-expression for improved function prediction of long non-coding RNAs.BMC bioinformatics · 2018Article
- Gene Ontology Enrichment Improves Performances of Functional Similarity of Genes.Scientific reports · 2018Article
- An improved approach to infer protein-protein interaction based on a hierarchical vector space model.BMC bioinformatics · 2018Article
- DDR: efficient computational method to predict drug-target interactions using graph mining and machine learning approaches.Bioinformatics (Oxford, England) · 2018Article
- Refine gene functional similarity network based on interaction networks.BMC bioinformatics · 2017Article
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Abstract
backgroundThe Gene Ontology (GO) is a dynamic, controlled vocabulary that describes the cellular function of genes and proteins according to tree major categories: biological process, molecular function and cellular component. It has become widely used in many bioinformatics applications for annotating genes and measuring their semantic similarity, rather than their sequence similarity. Generally speaking, semantic similarity measures involve the GO tree topology, information content of GO terms, or a combination of both.
resultsHere we present a new semantic similarity measure called TopoICSim (Topological Information Content Similarity) which uses information on the specific paths between GO terms based on the topology of the GO tree, and the distribution of information content along these paths. The TopoICSim algorithm was evaluated on two human benchmark datasets based on KEGG pathways and Pfam domains grouped as clans, using GO terms from either the biological process or molecular function. The performance of the TopoICSim measure compared favorably to five existing methods. Furthermore, the TopoICSim similarity was also tested on gene/protein sets defined by correlated gene expression, using three human datasets, and showed improved performance compared to two previously published similarity measures. Finally we used an online benchmarking resource which evaluates any similarity measure against a set of 11 similarity measures in three tests, using gene/protein sets based on sequence similarity, Pfam domains, and enzyme classifications. The results for TopoICSim showed improved performance relative to most of the measures included in the benchmarking, and in particular a very robust performance throughout the different tests.
conclusionsThe TopoICSim similarity measure provides a competitive method with robust performance for quantification of semantic similarity between genes and proteins based on GO annotations. An R script for TopoICSim is available at http://bigr.medisin.ntnu.no/tools/TopoICSim.R .
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