GO-Enrichment-Analysis-Demo web version: https://ycl6.github.io/GO-Enrichment-Analysis-Demo
topGO: Bioconductor, Paper
topGO (with enrichment_barplot
function): GitHub
clusterProfiler: Bioconductor, Paper, Documentation
enrichplot: Bioconductor
enrichR: CRAN
Demo Dataset: E-MTAB-8411 from The clock gene Bmal1 inhibits macrophage motility, phagocytosis, and impairs defense against pneumonia. PNAS. 2020;117(3):1543-1551.
License: GPL-3.0
In this tutorial, I will use the sequencing data from E-MTAB-8411 to demonstrate how to use topGO
, clusterProfiler
and Enrichr
via its R interface enrichR
to perform GO enrichment analysis.
This RNA-seq dataset contains 5 wild-type (GK1, GK3, GK5, GK7 and GK9) and 4 macrophage-specific Bmal1 knockout samples (GK2, GK4, GK6 and GK10). The fastq files were retreived from ArrayExpress and processed with the follow steps:
- Adapter and QC trimming with
BBDuk
- Mapping to Mouse genome (assemble MM10 and GENCODE M24 annotation) with
STAR
- Differential expression analysis with
DESeq2
We will perform the enrichment analysis using output from DESeq2
.
Download the result table from GitHub
cd /ngs/GO-Enrichment-Analysis-Demo
wget https://raw.githubusercontent.com/ycl6/GO-Enrichment-Analysis-Demo/master/DESeq2_DEG.txt
# From CRAN
install.packages(c("devtools", "data.table", "enrichR"))
# From Bioconductor
if(!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(c("org.Mm.eg.db", "clusterProfiler", "enrichplot"))
# From GitHub
# topGO with enrichment_barplot()
devtools::install_github("ycl6/topGO-feat", ref = "v2.41.0-barplot")