ClusterProfiler: enrichDGN failing to map gene ID

Question

[akansha.gitanjali]

I was trying to perform the functional enrichment analysis of my proteomics data using enrichDGN. (https://yulab-smu.github.io/clusterProfiler-book/chapter12.html#bar-plot) I converted my Uniprot id’s to Entrez id’s using entrez<-mapIds(org.Mm.eg.db, genesymbol, 'ENTREZID', 'SYMBOL', multiVals="first") but the list of entrez gene ID's is not mapping to enrichDGN. The below list is a small part of the list.

test <- c("109676", "20254", "380684", "73094", "218038", "56013")
edo <- enrichDGN(test)

--> No gene can be mapped.... --> Expected input gene ID: 3119,5308,23633,4204,3805,4247 --> return NULL...

my gene id's are in this format:

1 Ank2
2 Nefh
3 Sgip1
4 Srcin1
5 Ank2
6 Map1b
7 Ank2
8 Mapt
9 Gmip
10 Bsn

I checked these are indeed mouse entrez gene id's. Am I making any mistake here? Also posted this question on Github page but got no reply.

Answer 1

[antonioggsousa]

Hi,

Based on the function name:

Enrichment analysis based on the DisGeNET (http://www.disgenet.org/).

If you check the reference name: Janet et al. (2015) DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. Database bav028 http://database.oxfordjournals.org/content/2015/bav028.long

It says platform for the dynamical exploration of human diseases. If you try to give human gene entrez ids, it will work. My guess is that it only works for human gene entrez ids.

I hope this helps,

António