Question: How To Map Gene Id Or Gene Symbol To Locus
5
gravatar for Clark
8.3 years ago by
Clark50
Drexel University
Clark50 wrote:

Is there a convenient way to map Gene IDs to their locus on the human genome?

mapping • 8.4k views
ADD COMMENTlink modified 18 months ago by magic13620 • written 8.3 years ago by Clark50
1

And what IDs are you talking about?

ADD REPLYlink written 8.3 years ago by Michael Schubert6.9k

Entrez Gene IDs

ADD REPLYlink written 8.3 years ago by Clark50
12
gravatar for Ryan Dale
8.3 years ago by
Ryan Dale4.8k
Bethesda, MD
Ryan Dale4.8k wrote:

Ensembl supports a large number of accession formats; hopefully your Gene IDs will fall into one of these formats.

In general, to get all sorts of information on a list of accessions:

  • Go to Ensembl's BioMart
  • Choose Ensembl Genes 63 database
  • Choose the data set of interest (e.g., Homo sapiens genes)
  • In the left side panel, click on Filters
  • Unfold the GENES section on the resulting page
  • Check the ID list limit box, the origin of your gene accessions, (e.g., "Refseq Genomic ID(s)"), and either paste your accessions or upload a file
  • In the left side panel, click Attributes
  • Choose various values you want to see for each gene you've provided (e.g., under GENE, choose chromosome name, gene start, and gene end
  • Along the top nav bar, click Results
  • Download results, and click the Perl button for an example of how to use the API for programmatic access
ADD COMMENTlink written 8.3 years ago by Ryan Dale4.8k
2

the best advertisement for BioMart is that almost every how do i map X to Y on Biostar must be "use BioMart"

ADD REPLYlink written 8.3 years ago by Dave Bridges1.3k

Yup. Take home message: check the "related questions" box first :)

ADD REPLYlink written 8.3 years ago by Neilfws48k
4
gravatar for Sander Timmer
8.3 years ago by
Sander Timmer700
United Kingdom
Sander Timmer700 wrote:

You could use Ensembl Biomart for this. Just make a text file (or copy paste) the Gene IDs to the filter list (after selecting human, under filter go to Gene and select your Gene ID type). At the attributes page you can easily select what information for each gene should be selected.

ADD COMMENTlink written 8.3 years ago by Sander Timmer700
0
gravatar for magic136
18 months ago by
magic13620
magic13620 wrote:

bioDBnet is really a great web servise--> https://biodbnet-abcc.ncifcrf.gov/db/db2db.php reference:Gene Id Conversion Tool

ADD COMMENTlink written 18 months ago by magic13620
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