Can't convert dog ensembl IDs into gene names
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4214811 • 0
Last seen 5 months ago
United States

I usually use biomaRt to convert gene ids to symbols. However, this time the ensembl IDs I have (dog) do not match the ensembl ids of biomart dataset "clfamiliaris_gene_ensembl".

I also tried to use the ensembl web portal, the dog dataset is called ROS_Cfam_1.0 there. Looks like my genes do not match the genes from their dataset. My genes look like this:

"ENSCAFG00000045440" "ENSCAFG00000000001" "ENSCAFG00000000002" "ENSCAFG00000041462" "ENSCAFG00000000005"

Here is my biomaRt code:

ensembl <- useMart("ensembl")
ensembl <- useDataset("clfamiliaris_gene_ensembl",mart=ensembl)
gene_id <- getBM(attributes = c('ensembl_gene_id', 'external_gene_name'),
                 values = rownames(mydata),
                 filters = c('ensembl_gene_id'), mart = ensembl)
[1] ensembl_gene_id    external_gene_name
<0 rows> (or 0-length row.names)

it doesn't find my values. Should I use a different dataset for dogs?

biomaRt ensembldb • 321 views
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crossposted and answered from Ensembl support

Entering edit mode
Last seen 55 minutes ago
United States

If you search any of those IDs at the ensembl website, it indicates that they are specific to the Boxer breed, which is Dog10K_Boxer_Tasha, not Ros_cfam_10. And if you go to the Biomart webpage and try to find Dog10K_Boxer_Tasha as a dataset, it apparently isn't there. There might be a way around that, and if so Mike Smith will be along shortly to say what it is. But at a first glance, it seems you might not be able to map using the Ensembl IDs. Do you have gene symbols?

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