Unable to get all Uniprot IDs corresponding to Ensembl ID

Question

[Apprentice]

I want to convert Ensembl gene IDs to Uniprot IDs. I have used the biomaRt package in R and perform the following commands.

> ensembl <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")

> getBM(mart=ensembl,attributes=c("ensembl_gene_id","uniprot_gn_id"),filters="ensembl_gene_id",values="ENSG00000183955",uniqueRows=TRUE);

As a result, the following was output.

> id uniprot_gn_id

> 1 ENSG00000183955        C9JKQ0

> 2 ENSG00000183955        F8WC45

However, I think that this output is insufficient. Because the gene corresponding to Ensembl ID="ENSG00000183955" is KMT5A. Based on the following Uniprot site, I think that not only C9JKQ0 and F8WC45 but also A0A0C4DFR3, and Q9NQR1 should also be output. https://www.uniprot.org/uniprot/Q9NQR1

How can I get all Uniprot IDs in biomaRt? I would appreciate it if you could tell me.

[GenoMax]

You can also use UniProt's ID mapping tool here: https://www.uniprot.org/uploadlists/

Full data available in files here if you want to grep the information directly: https://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/idmapping/

Answer 1

[manaswwm]

In your case, via biomaRt, you are querying for the information available on the following page (if I am not mistaken): http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000183955;r=12:123384132-123409353. In order to get all the Uniprot IDs mentioned on this page, I would change the attributes that I am querying for to something like the following:

getBM(mart=ensembl,attributes=c("ensembl_gene_id","uniprotsptrembl", "uniprotswissprot"),filters="ensembl_gene_id",values="ENSG00000183955",uniqueRows=TRUE)

Here, uniprotsptrembl IDs are the "unreviewed" proteins and uniprotswissprot are the "reviewed" protein IDs. Using this I get:

  ensembl_gene_id uniprotsptrembl uniprotswissprot
1 ENSG00000183955                           Q9NQR1
2 ENSG00000183955          F8WC45                 
3 ENSG00000183955          C9JKQ0  

For ID A0A0C4DFR3, as you can see this is not listed on the gene page of Ensembl, but this is listed on Uniprot https://www.uniprot.org/uniprot/?query=ENSG00000183955&sort=score. I imagine a workaround here would be to use the REST-API feature of Uniprot directly and not biomaRt - https://www.ebi.ac.uk/proteins/api/doc/#!/proteins/getByCrossReference check this for more information

[Apprentice]

Thank you for your advice. As I answered above, I could get the information I wanted with the use of Uniprot ID mapping tool, but I will also try to use the REST-API feature of Uniprot that you told me.