organism choose of clusterProfiler

Question

[lifang5389]

Hi all,

I am very confusing about the parameter "organism" in the clusterProfilter. My organism is the Drosophila melanogaster (fruit fly) and I have checked that the ID I used are belong to D.melanogaster. But I got the error report "No gene can be mapped...." when "organism" is "dme". And it is very strange that when I changed the organism to "hsa", it works well.

head(gene)

[1] "33157" "3772540" "33202" "33374" "53544" "33396"

kk <- enrichKEGG(gene = gene, organism = "dme")

No gene can be mapped....

--> return NULL...

kk <- enrichKEGG(gene = gene, organism = "hsa")

summary(kk)

[shenwei356]

You can tag clusterProfiler to call the author Guangchuang Yu

Answer 1

[Guangchuang Yu]

If using the gene IDs you provided, it should not works for hsa as these gene IDs are not belong to human.

> g
[1] "33157"   "3772540" "33202"   "33374"   "53544"   "33396"
> select(org.Hs.eg.db, keys=g, keytype="ENTREZID", columns='ENTREZID')
Error in .testForValidKeys(x, keys, keytype, fks) :
  None of the keys entered are valid keys for 'ENTREZID'. Please use the keys method to see a listing of valid arguments.

---

You can check, http://rest.kegg.jp/link/pathway/dme, that dme in KEGG database are not using entrezgene ID. This is why your input gene IDs can't be mapped to any pathway of dme.

You can specify keyType and enrichKEGG will convert the IDs for you as it was documented in online vignettes.

> g = c("33157", "3772540", "33202", "33374", "53544", "33396")
> kk = enrichKEGG(g, organism='dme', keyType='ncbi-geneid', pvalueCutoff=1, qvalueCutoff=1)
> head(kk)
               ID Description GeneRatio  BgRatio     pvalue   p.adjust qvalue
dme04142 dme04142    Lysosome       1/1 118/3171 0.03721224 0.03721224     NA
         geneID Count
dme04142  33374     1

PLEASE DO READ THE VIGNETTE BEFORE POSTING QUESTION

Answer 2

[EagleEye]

Give it a try using GeneSCF.