Conversion of UniProt to Ensembl
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Recep • 0
@7c8fd686
Last seen 15 days ago
Germany

Hello, im new in bioinformatics and trying to convert uniprot ids to ensemble. i could install biomaRt and read the datas by using read.csv.

Now i need to convert the ids. But how can i do that? Could you share any documentation i couldnt find anything about that.

Thank you.

biomaRt ensembldb UniProt.ws • 189 views
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Note that this can also be done via the UniProt.ws package:

library(UniProt.ws)
up <- UniProt.ws()
univals <- head(keys(up, "UniProtKB"))
select(up, keys = univals, columns = c("accession", "id", "xref_ensembl"), keytype = "UniProtKB")
        From      Entry  Entry.Name                                                     Ensembl
1 A0A0C5B5G6 A0A0C5B5G6 MOTSC_HUMAN                                                        <NA>
2 A0A1B0GTW7 A0A1B0GTW7 CIROP_HUMAN                                          ENST00000637218.2;
3     A0JNW5     A0JNW5 UH1BL_HUMAN ENST00000279907.12 [A0JNW5-1];ENST00000356828.7 [A0JNW5-2];
4     A0JP26     A0JP26 POTB3_HUMAN  ENST00000611217.5 [A0JP26-1];ENST00000612601.2 [A0JP26-2];
5     A0PK11     A0PK11 CLRN2_HUMAN                                          ENST00000511148.2;
6     A1A4S6     A1A4S6 RHG10_HUMAN                                          ENST00000336498.8;

Though the IDs appear different...

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@james-w-macdonald-5106
Last seen 47 minutes ago
United States

I will provide an example below. But first, there is a vignette for biomaRt (actually two), and it has extensive examples of how to use the package. When you are trying to figure out how to use a package, reading the vignette (possible multiple times) should be your first step. What you want to do could easily be extrapolated from the information there, and if you want to learn how to use R/Bioconductor, reading examples and inferring how to do what you want from those examples is an invaluable skill.

Another skill is asking good questions. You don't say what species, so I am going to assume human. When asking a question, it's best to try to think of what relevant information somebody else might need to answer your question, and try to provide that.

## instanciate a mart object
> library(biomaRt)
> mart <- useEnsembl("ensembl","hsapiens_gene_ensembl")
## get some UniProt IDs
> library(UniProt.ws)
> univals <- head(keys(z, "UniProtKB"))
> univals
[1] "A0A0C5B5G6" "A0A1B0GTW7" "A0JNW5"     "A0JP26"     "A0PK11"    
[6] "A1A4S6"  
> getBM(c("ensembl_gene_id","uniprot_gn_id"), "uniprot_gn_id", univals, mart)
  ensembl_gene_id uniprot_gn_id
1 ENSG00000283654    A0A1B0GTW7
2 ENSG00000111647        A0JNW5
3 ENSG00000278699        A0JP26
4 ENSG00000278522        A0JP26
5 ENSG00000249581        A0PK11
6 ENSG00000071205        A1A4S6

It's important to remember to ask getBM to return your input IDs, so you know which Ensembl gene ID matches up to a given UniProt ID.

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