Question: Convert gene name to uniprot ID
1
gravatar for diablo82.26
4.7 years ago by
diablo82.2610
India
diablo82.2610 wrote:

i have a list of gene name in a file 

CHRNB2
EGR2
GCK
KRT14
LMNA
FGF3
TK2
ABCC8

how can i map them to uniprot ID ? 
P.S I tried Uniprot "ID mapping" (from-"GENEID" to-"UNIPROTKB AC").But it couldn't map.
Please sugg me what to do.Thnx

snp uniprot bioinformatics gene • 13k views
ADD COMMENTlink modified 4.7 years ago by Elisabeth Gasteiger1.5k • written 4.7 years ago by diablo82.2610
6
gravatar for networkbiothings
4.7 years ago by
United States
networkbiothings60 wrote:

Use Mygene.info.  You can do batch requests via post, or you can use the live API to do batch requests as well.

Here's how via the live API:

Click on the "Try API live!", select "gene query service".  Click on "post"

For "q" put in your gene names separated by a comma.

For "scopes" type "symbol" (without the quotation marks)

For "fields", use "symbol,entrezgene,uniprot" and any other parameter of interest

Click "try it" when done.

Result will be in the response body.

 

ADD COMMENTlink written 4.7 years ago by networkbiothings60
2

There is also a "mygene" python module available to use:

https://pypi.python.org/pypi/mygene

Usage examples on this id mapping tutorial:

http://nbviewer.ipython.org/gist/newgene/6771106

 

 

ADD REPLYlink written 4.7 years ago by Newgene340

very helpful.Thnx

ADD REPLYlink written 4.7 years ago by diablo82.2610
2
gravatar for hpmcwill
4.7 years ago by
hpmcwill1.1k
United Kingdom
hpmcwill1.1k wrote:

These look to be gene symbols not Entrez Gene identifiers, so identifier mapping for Entrez Gene would not work. However UniProt include most gene symbols and their various synonyms in their data, so a query should work and find the set of UniProtKB entries which match. For example:

  1. Go to the UniProt.org website
  2. Select "Protein Knowledgebase (UniProtKB)" for "Search in"
  3. For the "Query" enter 'gene:' followed by the gene symbol (e.g. "gene:CHRNB2")
  4. Click the "Search" button
  5. The results contain a list of UniProtKB entries matching this gene symbol (e.g. for CHRNB2)

I suspect you may have a specific species in mind so you might want to use additional terms to limit the results further.

Once you have worked out the form of the required query you could use the UniProt.org REST API to script the required queries and return only selected data.

 

ADD COMMENTlink written 4.7 years ago by hpmcwill1.1k

 UniProt.org REST API  work specifically for  UniProt IDs. Can you please demo using gene name?

ADD REPLYlink written 4.7 years ago by diablo82.2610
1
gravatar for aheinzel
4.7 years ago by
aheinzel110
Austria
aheinzel110 wrote:

your entries remind me of gene symbols. a couple of options are available, just to name a few:

  • David gene id conversion tool (choose official_gene_symbol during upload)
  • Ensembl biomart (use filters -> id list limit choose hgnc symbols to restrict the result to your genes of interest; select symbol and UniProt/TrEMBL Accession from the attributes section to get a mapping file
  • IdMapper ExcelAddIn (convert first from GeneSymbol to ENSG and from their further to UniprotID)
ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by aheinzel110
1
gravatar for Prakki Rama
4.7 years ago by
Prakki Rama2.2k
Singapore
Prakki Rama2.2k wrote:

Adding to the above list, you can also try  Biodbnet

 

ADD COMMENTlink written 4.7 years ago by Prakki Rama2.2k
1
gravatar for cdsouthan
4.7 years ago by
cdsouthan1.8k
cdsouthan1.8k wrote:

For the HGNC symbols its useful to go throught the Symbol Checker first   http://www.genenames.org/cgi-bin/symbol_checker

You can then do some cross-checks (e.g. see if the names are what you expect and if any symbols are outdated)

Then paste the HGNC: ID list column across to UniProt ID mapper

You can then filter by species and reviewed  (= Swiss-Prot)

(would be interesting if you ran a few thousand symbols through all the methods above and tell us how you got on!)

 

 

ADD COMMENTlink modified 4.7 years ago • written 4.7 years ago by cdsouthan1.8k

A note of caution, related to this question, from the results for the sequencial cross-reference restricts of Human Swiss-Prot, HGNC, Entrez Gene and Ensembl.  It thus looks like http://www.ncbi.nlm.nih.gov/pubmed/24939910 suggesting sub-19K numbers could be not far short of the mark, or at least nearer than the (conservative back then) 25K estimate a decade ago http://www.ncbi.nlm.nih.gov/pubmed/15174140

http://www.uniprot.org/uniprot/?query=%28organism%3A%22Homo+sapiens+[9606]%22%29+AND+reviewed%3Ayes&sort=score  = 20,213

http://www.uniprot.org/uniprot/?query=%28organism%3A%22Homo+sapiens+[9606]%22%29+AND+reviewed%3Ayes+AND+database%3A%28type%3Ahgnc%29&sort=score = 19,760

http://www.uniprot.org/uniprot/?query=%28organism%3A%22Homo+sapiens+[9606]%22%29+AND+reviewed%3Ayes+AND+database%3A%28type%3Ahgnc%29+AND+database%3A%28type%3Ageneid%29&sort=score = 18,768

http://www.uniprot.org/uniprot/?query=%28organism%3A%22Homo+sapiens+[9606]%22%29+AND+reviewed%3Ayes+AND+database%3A%28type%3Ahgnc%29+AND+database%3A%28type%3Ageneid%29+AND+database%3A%28type%3Aensembl%29&sort=score = 18,550

ADD REPLYlink modified 4.7 years ago • written 4.7 years ago by cdsouthan1.8k
1
gravatar for Elisabeth Gasteiger
4.7 years ago by
Geneva
Elisabeth Gasteiger1.5k wrote:

You should be able to obtain what you are looking for by following the instructions in this UniProt FAQ:

"Can I convert gene symbols to UniProtKB identifiers? How can I map UniProtKB IDs or ACs to gene symbols?" http://www.uniprot.org/faq/53

Please note that it is planned to extend the UniProt identifier mapping to gene symbols.

Don't hesitate to contact the UniProt helpdesk if you have additional questions.

ADD COMMENTlink written 4.7 years ago by Elisabeth Gasteiger1.5k
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