Enrichment of a specific GO term
1
1
Entering edit mode
10 weeks ago
barix ▴ 10

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!

rnaseq clusterprofiler • 209 views
ADD COMMENT
0
Entering edit mode
10 weeks ago

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

ADD COMMENT

Login before adding your answer.

Traffic: 1540 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6