ShinyGO is a graphical gene-set enrichment tool for animals and plants. It was developed based on a large annotation database derived from Ensembl and STRING-db for 59 plant, 256 animal, 115 archaeal and 1678 bacterial species. ShinyGO provides 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. It is an intuitive, graphical web application that can help researchers gain actionable insights from gene-sets. ShinyGO is available at http://ge-lab.org/go/. ShinyGO is based on several R/Bioconductor packages and a large annotation and pathway database compiled from many sources. It includes gene-sets for 315 organisms, including 184 at Ensembl, 59 from Ensembl Plants and 72 from Ensembl Metazoa. It also includes pathways from KEGG, MSigDB, GeneSetDB, Reactome, and many sources of verified or predicted miRNA and TF target genes. ShinyGO can retrieve pathway diagrams from KEGG via API access and visualize overlapping relationships among enriched gene-sets using a network view and hierarchical clustering tree. It also conducts statistical analysis on genomic features, such as chromosomal locations, exon numbers, transcript isoforms, and GC content. ShinyGO can also retrieve PPI networks from STRING and produce a custom link to an interactive, annotated network on the STRING web site. ShinyGO has more comprehensive gene-sets regarding TF and miRNA target genes for human, mouse and Arabidopsis compared to DAVID. It will continue to compile such information for other organisms and update the annotation database on a yearly basis. Older versions of the database will be made available to users to improve reproducibility. ShinyGO is an intuitive, graphical tool for enrichment analysis.ShinyGO is a graphical gene-set enrichment tool for animals and plants. It was developed based on a large annotation database derived from Ensembl and STRING-db for 59 plant, 256 animal, 115 archaeal and 1678 bacterial species. ShinyGO provides 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. It is an intuitive, graphical web application that can help researchers gain actionable insights from gene-sets. ShinyGO is available at http://ge-lab.org/go/. ShinyGO is based on several R/Bioconductor packages and a large annotation and pathway database compiled from many sources. It includes gene-sets for 315 organisms, including 184 at Ensembl, 59 from Ensembl Plants and 72 from Ensembl Metazoa. It also includes pathways from KEGG, MSigDB, GeneSetDB, Reactome, and many sources of verified or predicted miRNA and TF target genes. ShinyGO can retrieve pathway diagrams from KEGG via API access and visualize overlapping relationships among enriched gene-sets using a network view and hierarchical clustering tree. It also conducts statistical analysis on genomic features, such as chromosomal locations, exon numbers, transcript isoforms, and GC content. ShinyGO can also retrieve PPI networks from STRING and produce a custom link to an interactive, annotated network on the STRING web site. ShinyGO has more comprehensive gene-sets regarding TF and miRNA target genes for human, mouse and Arabidopsis compared to DAVID. It will continue to compile such information for other organisms and update the annotation database on a yearly basis. Older versions of the database will be made available to users to improve reproducibility. ShinyGO is an intuitive, graphical tool for enrichment analysis.