clusterProfiler for KEGG enrichment (non-model species) Over-Representation Analysis

Question

[1215045934]

Hi there! I would like to perform KEGG enrichment with some differentially expressed gene data from RNAseq data. I am working on a non-model organism.

I have 1) KEGG to GeneName Mapping

head(expr5_FS_final)
    KEGG unigene_FS
1 K02727  FS_gene_1
2 K17277  FS_gene_3
3 K17307 FS_gene_10
4 K14453 FS_gene_11
5 K14700 FS_gene_11
6 K14701 FS_gene_11

2) A list of genes of interest (DEGs)

head(DEG)
  DEG
1 FS_gene_1
2 FS_gene_38
3 FS_gene_101

I used the the list of DEG to grep KEGG to GeneName Mapping file, then got a KEGG to GeneName Mapping file just for DEGs.

head(DEG_KEGG)
  KEGG DEG
1 K02727  FS_gene_1
2 K17277  FS_gene_1
3 K17307 FS_gene_38
...

Then I use enr_results <- enrichKEGG(DEG_KEGG$KEGG, organism='ko', minGSSize = 1, pvalueCutoff = 0.05, qvalueCutoff = 0.05) to do KEGG enrichment.

I also tried enr_results2 <- enricher(DEG$DEG , TERM2GENE=expr5_FS_final, pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05, minGSSize = 5)

Which one is correct? Could some one help me have a look?

Thanks a lot!

Answer 1

[Di Wu]

I think organism='ko' is not correct. After '?enrichKEGG', it seems that we should check the list in 'https://www.genome.jp/kegg/catalog/org_list.html'