Question: Converting Hgnc Gene Symbol To Gi Number
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gravatar for hallister01
6.6 years ago by
hallister010 wrote:

I am trying to process a large list of HGNC gene symbols and retrieve their respective GI numbers and put them into an excel table.

Can this be done with E utilities? Does anyone have a script for perl?

convert • 2.7k views
ADD COMMENTlink modified 5.3 years ago by Biostar ♦♦ 20 • written 6.6 years ago by hallister010
2

"and put them into an excel table. " ... please, DON'T DO THAT . http://www.biomedcentral.com/1471-2105/5/80

ADD REPLYlink written 6.6 years ago by Pierre Lindenbaum126k

It always astounds me that people want to use GI numbers... Why??! Why not use an accession + version number?

ADD REPLYlink written 6.6 years ago by sarahhunter600
1
gravatar for Pierre Lindenbaum
6.6 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum126k wrote:

Use http://www.genenames.org/cgi-bin/hgnc_downloads

select "Approved Symbol" and "Entrez Gene ID"

http://www.genenames.org/cgi-bin/hgnc_downloads?col=gd_app_sym&col=gd_pub_eg_id&status_opt=2&where=&order_by=gd_hgnc_id&format=text&limit=&submit=submit

ADD COMMENTlink written 6.6 years ago by Pierre Lindenbaum126k

But EGIDs are not GIs, you need to EGID > RefSeq > GI

ADD REPLYlink written 6.6 years ago by cdsouthan1.8k

Thanks for the reply but what I need to accomplish is to process my list of HGNC gene symbols and have their GI numbers assigned.

I need GI numbers for my mass spec program and NOT gene ID's

ADD REPLYlink written 6.6 years ago by hallister010

Your ms program should be mapping to UniProt IDs, that simplifies things

ADD REPLYlink written 6.6 years ago by cdsouthan1.8k
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