Missing Gene Symbols From Mgi With Biomart (Mouse)

Question

[traversc]

I'm trying to use biomaRt to get attributes for a bunch of genes. When I try it, I notice that there are some missing values. Can someone tell me why?

Ex.:

library(biomaRt)
mart <- useMart(biomart="ensembl", dataset="mmusculus_gene_ensembl")
results <- getBM(attributes = c("gene_biotype", "mgi_symbol"), filters = "mgi_symbol", values = "Gm4890", mart = mart)

Yet I can see the gene plainly here: http://www.informatics.jax.org/marker/MGI:3779445

Answer 1

[Emily]

I just did your query and got a result:

lincRNA    Gm4890

How many IDs did you use in your query? Are you using the latest version (74), because the name Gm4890 wasn't assigned in previous databases?

[traversc]

How do I check which version of ensembl I am using with biomaRt? I assumed it would use the latest, since it pulls from the online database?

I don't think that is the issue anyway, because these IDs came from fairly old reference files.

[Emily]

It definitely works with the current database, because I tried it.

How many IDs did you use in your query?

[traversc]

Thank you Emily.

I figured out the problem in case anyone was wondering... I just needed to update Bioconductor

/slaps forehead

[Aynur]

Hello, I am also using biomaRt on R, and have some ensemble ids without mgi symbol.

Updating did not solve the problem.

Can some one help me with this?

Thanks.

[Adriano.Biasini]

Have you found a solution to this problem? I also noticed that from a list of 46,000 MGI loci, only 38,000 are converted to ensembl genes even after updating to the most recent version of bioconductor.

[Emily]

Can you send the list of ids to [e-mail] and we can look into it.

[sakshichauhan2]

I am facing the same issue. Out of 54146 ensembl_gene_ids, I get 50663 Mgi_gene_symbols. Did you find any solution?