How to Use clusterProfiler

What is clusterProfiler?

clusterProfiler is a software tool used for performing functional enrichment analysis, such as GO analysis and pathway analysis, on gene lists.

Gene lists are often obtained by identifying differentially expressed genes (DEGs) from data such as RNA-Seq analysis.

This page explains how to use and install clusterProfiler.

Installing clusterProfiler

First, if R is not installed, you need to install R. (This is an example using Homebrew for installation.)

$ brew install r

Start R and run the following commands to install BiocManager and clusterProfiler.

> if (!requireNamespace("BiocManager", quietly=TRUE)) > install.packages("BiocManager") > BiocManager::install("clusterProfiler")

Run the following commands, and if no errors are displayed, the installation was successful.

> library(clusterProfiler)

Let's also prepare the necessary annotations. The following is for humans.

> BiocManager::install("org.Hs.eg.db")

Run the following commands, and if no errors are displayed, the installation was successful.

> library(org.Hs.eg.db)

Data Preparation

The gene list is prepared using tools such as edgeR. Be sure to obtain both the list of all genes (all_genes) and the list of differentially expressed genes (degs) as shown below.

> all_genes <- rownames(result) > degs <- rownames(result[result$FDR<0.05,])

For more details on how to use edgeR, please refer to this page.

Performing GO Analysis

You can perform functional enrichment analysis on the Biological Process category of Gene Ontology using the following command.

> ego <- enrichGO(gene=degs, universe=all_genes, OrgDb=org.Hs.eg.db, ont="BP", pvalueCutoff=0.01, qvalueCutoff=0.05)

The output is as follows.

ID Description ... geneID Count GO:0045930 GO:0045930 negative regulation of mitotic cell cycle ... ENSG00000010244/ENSG00000108691/ENSG0000019878... 5 GO:1901991 GO:1901991 negative regulation of mitotic cell cycle phas... ... ENSG00000010244/ENSG00000108691/ENSG0000019878... 4 GO:0045786 GO:0045786 negative regulation of cell cycle ... ENSG00000010244/ENSG00000108691/ENSG0000019878... 5 GO:0090329 GO:0090329 regulation of DNA-templated DNA replication ... ENSG00000198783/ENSG00000005156/ENSG00000172716 3 GO:1901988 GO:1901988 negative regulation of cell cycle phase transi... ... ENSG00000010244/ENSG00000108691/ENSG0000019878... 4 GO:0010948 GO:0010948 negative regulation of cell cycle process ... ENSG00000010244/ENSG00000108691/ENSG0000019878... 4

As shown above, the functional enrichment analysis resulted in a list of Gene Ontology terms that are significantly overrepresented in the list of differentially expressed genes compared to the entire set of genes.

RNA-Seq Data Analysis Software

With our RNA-Seq data analysis software, you won't need to outsource or rely on collaborators. You can start analyzing the data yourself right away, without the need for high-spec computers or knowledge of Linux commands.

Users can perform gene expression quantification, identification of differentially expressed genes, gene ontology(GO) analysis, pathway analysis, as well as drawing volcano plots, MA plots, and heatmaps.

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