Question: check if ensembl_gene_id maps to primary assembly
gravatar for Mo Sander
6.3 years ago by
Mo Sander50
United Kingdom
Mo Sander50 wrote:

I am looking for a method to determine if a given ensembl_gene_id maps to the primary assembly or an alternate/patched chromosome.

For example, I have multiple ensembl_gene_ids for TNF alpha, but only one maps to the primary assembly:

  • ENSG00000228321
  • ENSG00000206439
  • ENSG00000232810
  • ENSG00000228978
  • ENSG00000228849
  • ENSG00000228321
  • ENSG00000206439
  • ENSG00000232810 * maps to primary assembly
  • ENSG00000228978
  • ENSG00000228849

Is there an API or web service that provides this functionality?

assembly gene • 2.1k views
ADD COMMENTlink modified 5.6 years ago by Biostar ♦♦ 20 • written 6.3 years ago by Mo Sander50
gravatar for Emily_Ensembl
6.3 years ago by
Emily_Ensembl21k wrote:

You could use BioMart. Just filter by your list of IDs and the location, selecting all the normal chromosome numbers. Alternatively, filter by IDs and get the chromosomes as attributes. There's a help video on using BioMart here.

ADD COMMENTlink written 6.3 years ago by Emily_Ensembl21k
gravatar for Bert Overduin
6.3 years ago by
Bert Overduin3.7k
Edinburgh Genomics, The University of Edinburgh
Bert Overduin3.7k wrote:

Or use the REST API: will give you:

{"source":"ensembl_havana","object_type":"Gene","logic_name":"ensembl_havana_gene","species":"homo_sapiens","description":"tumor necrosis factor [Source:HGNC Symbol;Acc:HGNC:11892]","display_name":"TNF","biotype":"protein_coding","end":31617784,"seq_region_name":"CHR_HSCHR6_MHC_MANN_CTG1","db_type":"core","strand":1,"id":"ENSG00000228321","start":31615015}

and will give you:

{"source":"ensembl_havana","object_type":"Gene","logic_name":"ensembl_havana_gene","species":"homo_sapiens","description":"tumor necrosis factor [Source:HGNC Symbol;Acc:HGNC:11892]","display_name":"TNF","biotype":"protein_coding","end":31578336,"seq_region_name":"6","db_type":"core","strand":1,"id":"ENSG00000232810","start":31575567}

As you can see the "seq_region_name" gives you name of the chromosome on which the gene in question is located.

ADD COMMENTlink modified 13 months ago by _r_am31k • written 6.3 years ago by Bert Overduin3.7k
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