Mapping HGNC ID to uniprot ID

Question

[Paul]

I have a list of HGNC IDs and wanted to map it to uniprot.swissprot ID.

The tools I have used so far are

• David tool for conversion of IDs,
• Biomart (R package) and
• Mygene.info (R package)

But the problem with the first two tools (David and Biomart) is that they accept only smaller gene list as an input and I have 60,000 list of genes. So, I have also tried Mygene.info as an R package (As I have better understanding of R than python or any other programming languages). But when I try to give a gene list as an input in (mygene) package,

res <- queryMany(c('1053_at', '117_at', '121_at', '1255_g_at', '1294_at'),scopes='reporter', species='human')

it shows

Error: is.request(y) is not TRUE

Why is the error showing, whenever I am inputting a gene-list. Please help me figure out where the problem is and how it can be solved?

Thanks in advance.

[User 59]

I think it needs to be pointed out that you're not passing in a gene list there, they're not HGNC identifiers, they're Affymetrix probeset identifiers, which is not really the same thing at all...

[Sean Davis]

I'd suggest sticking with biomaRt and just getting all genes. You can then match up or filter your results in R. Or am I misunderstanding your problem?

[Paul]

Yeah but then it takes only limited number of genes(smaller gene list), doesn't work when I try to do it for more number of genes. :( How do I do for larger gene list? Around 60,000 genes. The biomart package takes atmax 300 genes n then shows connection timed out

[Sean Davis]

I'm suggesting not supplying any filter values. Just have biomaRt pull the data for all the genes.

[Paul]

Yeah just ran biomaRt without any filters (ID <- getBM(attributes= c("hgnc_symbol", "uniprot_genename","uniprot_swissprot"),mart= mart)). Got a list of 35353 genes. So, now I have to map it with my gene list, right? Correct me if I am wrong. Thanks a lot. It solved the problem.

[Sean Davis]

In R, this is a subsetting, match(), or merge() operation that will likely take just a second or two to run.

[Paul]

If you don't mind could you please add your answer with an example because I dont want to leave any gap in my understanding.

Answer 1

[Elisabeth Gasteiger]

Have you tried the UniProt IDmapping tool? http://www.uniprot.org/uploadlists

It works with HGNC identifiers (e.g. HGNC:9884) or gene symbols (e.g. RB1), however not with Affymetrix probeset identifiers.