Enrichment of a specific GO term

Question

[barix]

Hi all,

I'm using clusterProfiler for gene enrichment analysis and would like to check how enriched are specific GO terms.

For example, I have df with DEx genes (experimental vs control) and would like to see how GO:0043066 is enriched, not just which GO terms are enriched.

My approach is following:

• intersections between list of upregulated genes in experimental group and genes from GO term of interest
• setting universe in enrichGO function as all of my expressed genes

   dnarepair.genes <- intersect(DEG$endo$genes, go_list$dnarepair)
    X <- enrichGO(dnarepair.genes, 
                  universe=allgenes, #(rownames(seurat)[Matrix::rowMeans(seurat$RNA@data !=0) >= 0.1])
                  ont = 'ALL',
                  keyType = "SYMBOL", 
                  pvalueCutoff = 0.05,
                  OrgDb = org.Mm.eg.db)

Any suggestions? Thanks!

Answer 1

[Kevin Blighe]

In this case, I would favour to do the enrichment via fGSEA and using your own custom-created GO:0043066 gene-set, or that automatically retrieved via msigdbr

Mouse gene-sets are also available via WEHI: GSEA with mouse RNAseq data

Kevin