I have roughly mouse 200 DEGs with Ensembl IDs and would like to convert them to gene symbols/names. I've tried gconvert from gproflier2 as follows;
t<-gconvert(gene, organism = "mmusculus", target = "ENSG", filter_na = T)
and bioMart
ensembl <- useMart("ensembl", dataset="mmusculus_gene_ensembl")
gene <- getBM(attributes=c('ensembl_gene_id','external_gene_name'), filters = 'ensembl_gene_id', values = mouse_gene_ids, mart = ensembl)
with no luck. I checked some of these DEGs (e.g. ENSMUSE00000199608) in Ensembl browser and did see the gene but not in gProfiler web site. Am I missing something here or are there any ways to convert Ensembl gene ID of these DEGs to gene names/symbols in R ?
Using the info @i.sudbery's good eye caught. You should change your filter. To find out which filter to use
library(biomaRt)
mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL")
m_ensembl = useDataset(dataset = "mmusculus_gene_ensembl", mart = mart)
h_ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
lF <- listFilters(m_ensembl)
lF[grep("exon", lF$name),]
This is the filter you should use.
name description
55 ensembl_exon_id Exon ID(s) [e.g. ENSMUSE00000097910]
So now, if you run again but use ensembl_exon_id as filter, you should get the gene names.
Just want to add that you can use the searchFilters() function to find the appropriate filters in one step e.g.
> searchFilters(m_ensembl, "exon")
name description
55 ensembl_exon_id Exon ID(s) [e.g. ENSMUSE00000097910]
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look at this post
Tried the script on the post but did not work. I get NA. Ensembl transcript ID's heading is ENSUMST, whereas my geens have ENSMUSE.
Can you post what error you are getting ? also
head(mouse_gene_ids)output.I am not getting any error but zero contents. Output of is as follows;
The id you have posted is an exon id, not a gene id.
Ok got it but I can't figure out why I got a transcript ID instead of gene ID ? I used featureCounts with GTFattrType ="gene_id" script;
This will be an new question.