ShinyGO: a graphical gene-set enrichment tool for animals and plants
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Abstract
MOTIVATION: Gene lists are routinely produced from various omic studies. Enrichment analysis can link these gene lists with underlying molecular pathways and functional categories such as gene ontology (GO) and other databases. RESULTS: To complement existing tools, we developed ShinyGO based on a large annotation database derived from Ensembl and STRING-db for 59 plant, 256 animal, 115 archeal and 1678 bacterial species. ShinyGO's novel features include graphical visualization of enrichment results and gene characteristics, and application program interface access to KEGG and STRING for the retrieval of pathway diagrams and protein-protein interaction networks. ShinyGO is an intuitive, graphical web application that can help researchers gain actionable insights from gene-sets. AVAILABILITY AND IMPLEMENTATION: http://ge-lab.org/go/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Gene ontology analysis identified 219 biological processes with FDR below 0.05, with top findings in nervous system development, synapse assembly, and synapse organization.
“Gene ontology analysis conducted in ShinyGO18 identified 219 biological processes with FDR < 0.05, with top findings involved in nervous system development (q=1.20×10−10), and synapse assembly (q=9.75×10−9) and organization (q=9.75×10−9)”
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- Authors
- Ge, S. X., Jung, D., & Yao, R.
- Affiliations
- Department of Mathematics and Statistics , Brookings, SD 57007, USA
- South Dakota State University (US)
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2019-12-27
- Volume
- 36
- Issue
- 8
- Pages
- 2628-2629
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- PMC
- PMC7178415
- OpenAlex
- W2997022986
- Cited by
- 5,270
- References
- 4
- Citations by year
- 2026: 1074 · 2025: 1417 · 2024: 1204 · 2023: 783 · 2022: 419 · 2021: 235 · 2020: 110 · 2019: 23 · 2018: 3
- FWCI
- 65.41
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Bioinformatics (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- YUHSpace (Yonsei University Medical Library) (submittedVersion, cc-by-nc-nd)
- Funders
- National Institutes of Health (GM083226)
- National Science Foundation/EPSCoR (IIA-1355423)
- State of South Dakota
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Biomedical Text Mining and Ontologies
- Keywords
- gene set enrichment analysis, Gene Ontology, pathway visualization, protein-protein interaction network, web application, annotation database, Ensembl, strings, plants, animals, archaea, bacteria
- MeSH terms
- Animals, Probability, Software, Databases, Factual, Computational Biology, Internet, Databases, Genetic, Gene Ontology
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