Question: Mapping HGNC ID to uniprot ID
2
gravatar for Paul
3.8 years ago by
Paul80
India
Paul80 wrote:

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 (Rpackage) and 

Mygene.info (Rpackage)

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..

rna-seq uniprot gene • 2.2k views
ADD COMMENTlink modified 21 months ago • written 3.8 years ago by Paul80
3

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...

ADD REPLYlink written 3.8 years ago by Daniel Swan13k
1

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?  

ADD REPLYlink written 3.8 years ago by Sean Davis25k
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
ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Paul80
1

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

ADD REPLYlink written 3.8 years ago by Sean Davis25k

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.

ADD REPLYlink written 3.8 years ago by Paul80
2

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

ADD REPLYlink written 3.8 years ago by Sean Davis25k

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.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by Paul80
0
gravatar for Elisabeth Gasteiger
3.8 years ago by
Geneva
Elisabeth Gasteiger1.6k wrote:

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.

ADD COMMENTlink written 3.8 years ago by Elisabeth Gasteiger1.6k
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