How To Map Gene Id Or Gene Symbol To Locus

Question

[Clark]

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

[Michael Schubert]

And what IDs are you talking about?

[Clark]

Entrez Gene IDs

Answer 1

[Ryan Dale]

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

[Dave Bridges]

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

[Neilfws]

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

Answer 2

[Sander Timmer]

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.

Answer 3

[magic136]

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