UniProt ID, genes

Question

[Rob]

Hi friends,

How can I download the UniProt ID for protein coding genes? I have about 20000 genes and it is hard to just search them one by one. IS there any code for it?

I have a code to download gene names through the DESeq2 workflow, however it does not give UniProt ID.

attributeNames <-c("ensembl_gene_id","external_gene_name","hgnc_symbol", "chromosome_name","description", "entrezgene_id")

filterValues <- rownames(result_DESeq2)

Annotations <- getBM(attributes=attributeNames, filters =
                       "ensembl_gene_id",values = filterValues,
                     mart=useMart(biomart="ensembl",
                                  dataset="hsapiens_gene_ensembl"))

resAnnotated <- as.data.frame(res) %>% 
  rownames_to_column("ensembl_gene_id") %>% left_join(Annotations,
                                                      "ensembl_gene_id") %>% dplyr::rename(logFC=log2FoldChange, FDR=padj)

Thanks

[GenoMax]

You can download UniProt ID's from their site. Customize columns you need or additionally filter using the options in left column.

[Rob]

Thank you GenoMax

[seidel]

The workflow is using the biomaRt library (as @Hamid points out below). If you create the mart, you can query it for the attributes in can return using listAttributes(mart), and you'll see the roughly 3000 or so things you can get back, including UniProt IDs.

[Rob]

Thanks seidel

Answer 1

[Antonio R. Franco]

Give a try to the Uniprot convertion database

[Elisabeth Gasteiger]

Indeed, the UniProt IDmapping/batch retrieve service at https://www.uniprot.org/id-mapping has an option to map from Gene names (idealy restricted to an organism) to UniProtKB. Several download formats are available.

[Antonio R. Franco]

in addition, you can get the sequences, GO and KEGG terms, and a long set of other features

Answer 2

[Hamid Ghaedi]

I assume you have a list of Ensembl gene ids (let's call it "ens_gene_ids"), the following should give you the UniProt ids for Ensembl ids that code for proteins and have an entry in UniProt:

library(biomaRt)
mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
genes <- getBM(filters= "ensembl_gene_id", 
               attributes= c("ensembl_gene_id","hgnc_symbol", "uniprot_gn_id"),
               values= ens_gene_ids, 
                 mart= mart)

[Rob]

Thank you Hamid it was helpful.