ShinyGO: a graphical gene-set enrichment tool for animals and plants

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...

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Bibliographic Details
Published in	Bioinformatics Vol. 36; no. 8; pp. 2628 - 2629
Main Authors	Ge, Steven Xijin, Jung, Dongmin, Yao, Runan
Format	Journal Article
Language	English
Published	England Oxford University Press 15.04.2020
Subjects	Animals Applications Notes Computational Biology Databases, Factual Databases, Genetic Gene Ontology Internet Probability Software
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Abstract	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.
AbstractList	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. 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. http://ge-lab.org/go/. Supplementary data are available at Bioinformatics online. 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.MOTIVATIONGene 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.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.RESULTSTo 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.http://ge-lab.org/go/.AVAILABILITY AND IMPLEMENTATIONhttp://ge-lab.org/go/.Supplementary data are available at Bioinformatics online.SUPPLEMENTARY INFORMATIONSupplementary data are available at Bioinformatics online. 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.
Author	Ge, Steven Xijin Jung, Dongmin Yao, Runan
AuthorAffiliation	2 Severance Biomedical Science Institute, Yonsei University College of Medicine , Seoul 03722, South Korea 1 Department of Mathematics and Statistics , Brookings, SD 57007, USA
AuthorAffiliation_xml	– name: 1 Department of Mathematics and Statistics , Brookings, SD 57007, USA – name: 2 Severance Biomedical Science Institute, Yonsei University College of Medicine , Seoul 03722, South Korea
Author_xml	– sequence: 1 givenname: Steven Xijin orcidid: 0000-0001-7406-3782 surname: Ge fullname: Ge, Steven Xijin email: gexijin@gmail.com organization: Department of Mathematics and Statistics, Brookings, SD 57007, USA – sequence: 2 givenname: Dongmin surname: Jung fullname: Jung, Dongmin organization: Department of Mathematics and Statistics, Brookings, SD 57007, USA – sequence: 3 givenname: Runan surname: Yao fullname: Yao, Runan organization: Department of Mathematics and Statistics, Brookings, SD 57007, USA
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/31882993$$D View this record in MEDLINE/PubMed
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References	Khatri (2023013110255630100_btz931-B8) 2012; 8 Aken (2023013110255630100_btz931-B1) 2017; 45 Huang da (2023013110255630100_btz931-B6) 2009; 4 Fabregat (2023013110255630100_btz931-B5) 2016; 44 Liberzon (2023013110255630100_btz931-B12) 2015; 1 Araki (2023013110255630100_btz931-B2) 2012; 2 Bolser (2023013110255630100_btz931-B4) 2017; 1533 Kuleshov (2023013110255630100_btz931-B9) 2016; 44 Lai (2023013110255630100_btz931-B10) 2016 Ashburner (2023013110255630100_btz931-B3) 2000; 25 Kanehisa (2023013110255630100_btz931-B7) 2017; 45 Lai (2023013110255630100_btz931-B11) 2012; 28 Szklarczyk (2023013110255630100_btz931-B13) 2015; 43 Yi (2023013110255630100_btz931-B14) 2013; 41
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Snippet	Abstract Motivation Gene lists are routinely produced from various omic studies. Enrichment analysis can link these gene lists with underlying molecular... Gene lists are routinely produced from various omic studies. Enrichment analysis can link these gene lists with underlying molecular pathways and functional...
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SourceType	Open Access Repository Aggregation Database Index Database Enrichment Source Publisher
StartPage	2628
SubjectTerms	Animals Applications Notes Computational Biology Databases, Factual Databases, Genetic Gene Ontology Internet Probability Software
Title	ShinyGO: a graphical gene-set enrichment tool for animals and plants
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