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

Author:

Ge Steven Xijin1ORCID,Jung Dongmin12,Yao Runan1

Affiliation:

1. Department of Mathematics and Statistics, Brookings, SD 57007, USA

2. Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul 03722, South Korea

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.

Funder

National Institutes of Health

National Science Foundation/EPSCoR

State of South Dakota

Publisher

Oxford University Press (OUP)

Subject

Computational Mathematics,Computational Theory and Mathematics,Computer Science Applications,Molecular Biology,Biochemistry,Statistics and Probability

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