Download STRING database with Protein name

Question

[LimMo]

Hi all,

I need to work with STRING database, once I download protein.links.full.v10.5.txt I got something like that:

ENSP00000000233 ENSP00000263431 0 0 0 0 0 0 53 0 176 0 0 0 128 260
ENSP00000000233 ENSP00000353863 0 0 0 0 0 0 52 0 106 0 0 0 93 164
ENSP00000000233 ENSP00000342026 0 0 0 0 0 0 53 0 71 0 0 97 67 159
ENSP00000000233 ENSP00000240874 0 0 0 0 0 0 0 0 170 0 0 46 64 194

My question is there anyway to download/convert those ensemble protein as a protein name? because I need to work with their name rather then IDs.

Any help will be appreciated.

[Sej Modha]

You can use BioMart to convert Ensembl IDs to the gene names.

[LimMo]

Could you please guide me how/where exactly to do that, it's my first time to try it.

Answer 1

[thomaskuilman]

Here is an R-based solution:

> test
[1] "ENSP00000263431" "ENSP00000353863" "ENSP00000342026" "ENSP00000240874"
> library("biomaRt")
> ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl")
> conversion.table <- getBM(attributes = c("ensembl_peptide_id", "hgnc_symbol"),
                            filters = "ensembl_peptide_id" , values = list(test),
                            mart = ensembl)
> head(conversion.table)
  ensembl_peptide_id hgnc_symbol
1    ENSP00000240874       KALRN
2    ENSP00000263431       PRKCG
3    ENSP00000342026       PRDX6
4    ENSP00000353863      ZNF148

If you want to get all the possible attributes that can be used in the getBM function, you can get these using

> listAttributes(ensembl)

Similarly, using

> listFilters(ensembl)

you can obtain all the possible filters.

[LimMo]

I got this error The query to the BioMart webservice returned an invalid result: biomaRt expected a character string of length 1. Please report this to the mailing list.

[thomaskuilman]

As pointed out here and here, this is likely due to a server being temporarily down. I am not sure where you are, but you can try any of these mirrors

https://www.ensembl.org/

https://uswest.ensembl.org/

https://useast.ensembl.org/

https://asia.ensembl.org/

by adding the arguments host = "www.ensembl.org", ensemblRedirect = FALSE to your useMart call. Obviously, you can use any of the hosts instead of the (standard) one mentioned ("www.ensembl.org").

[LimMo]

Thanks a lot now it's work well with me, the problem was from the type of the data not from the server. But I notice that a lot of the Ensembl protein were ignored, so, for example, I enter around 11 million Ensembl protein and I got after conversion around 39 thousand!!