Gene Ontology Enrichment Analysis using ShinyGO (an R Shiny Server)

This tutorial explains how to perform Gene Ontology (GO) Enrichment Analysis using ShinyGO (a cloud R Shiny server). ShinyGO is an online graphical interface tool for gene-set enrichment analysis. It is an open-source program written using R language and enveloped with Shiny and BioConductor packages. The online tool runs on the Shiny cloud server; whereas the source code is hosted at the GitHub repository.

In this tutorial, I have used the Gene Set Enrichment Analysis (GSEA)/Molecular Signatures Database (MSigDB) to retrieve a list of gene IDs for human liver cancer. Moreover, I have used the ShinyGO 0.77 (version 0.77) tool for gene enrichment analysis. The current beta release is ShinyGO 0.80 (as on July 5, 2023).

The ShinyGO tool produces following results: Gene Ontology (GO) Enrichment, Fold Enrichment Chart, Hierarchical Tree Diagram, Gene Network Graph, KEGG Pathway Map, Genes Position, Density & Bar Plot, Genome Position, Motif in Promoter, STRING Protein-Protein Interaction (PPI) Network of Differently Expressed Gene (DEG).

Resource URLs:
ShinyGO: http://bioinformatics.sdstate.edu/go/
ShinyGO (Mirror): http://ge-lab.org/go/
ShinyGO (GitHub): https://github.com/gexijin/shinygo
ShinyGO (Database): http://bioinformatics.sdstate.edu/data/
GSEA: https://www.gsea-msigdb.org/gsea/inde...

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