ArticleBMC genomics2016
InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- A Literature Review of Gene Function Prediction by Modeling Gene Ontology.Frontiers in genetics · 2020Review
- TS-GOEA: a web tool for tissue-specific gene set enrichment analysis based on gene ontology.BMC bioinformatics · 2019Article
- Multi-domain semantic similarity in biomedical research.BMC bioinformatics · 2019Article
- Predicting disease-related phenotypes using an integrated phenotype similarity measurement based on HPO.BMC systems biology · 2019Article
- Article
- Improving the measurement of semantic similarity by combining gene ontology and co-functional network: a random walk based approach.BMC systems biology · 2018Article
- Identifying term relations cross different gene ontology categories.BMC bioinformatics · 2017Article
- Refine gene functional similarity network based on interaction networks.BMC bioinformatics · 2017Article
- Constructing an integrated gene similarity network for the identification of disease genes.Journal of biomedical semantics · 2017Article
- Multiple kernels learning-based biological entity relationship extraction method.Journal of biomedical semantics · 2017Article
- Dynamically analyzing cell interactions in biological environments using multiagent social learning framework.Journal of biomedical semantics · 2017Article
- Investigations on factors influencing HPO-based semantic similarity calculation.Journal of biomedical semantics · 2017Article
- A novel method to identify pre-microRNA in various species knowledge base on various species.Journal of biomedical semantics · 2017Article
- DisSetSim: an online system for calculating similarity between disease sets.Journal of biomedical semantics · 2017Article
- Erratum to: InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology.BMC genomics · 2017Article
- Predicting disease-related genes using integrated biomedical networks.BMC genomics · 2017Article
- OAHG: an integrated resource for annotating human genes with multi-level ontologies.Scientific reports · 2016Article
Corrections and comments
- Erratum issued
Authors and funding
7 authors.
Funding
Abstract
backgroundThe Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take into account all the rich information in GO. Similarly, using these existing methods, web-based applications have been constructed to compute gene functional similarities, and to provide pure text-based outputs. Without a graphical visualization interface, it is difficult for result interpretation.
resultsWe present InteGO2, a web tool that allows researchers to calculate the GO-based gene semantic similarities using seven widely used GO-based similarity measurements. Also, we provide an integrative measurement that synergistically integrates all the individual measurements to improve the overall performance. Using HTML5 and cytoscape.js, we provide a graphical interface in InteGO2 to visualize the resulting gene functional association networks.
conclusionsInteGO2 is an easy-to-use HTML5 based web tool. With it, researchers can measure gene or gene product functional similarity conveniently, and visualize the network of functional interactions in a graphical interface. InteGO2 can be accessed via http://mlg.hit.edu.cn:8089/ .
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.