Convert Ensembl Transcript Ids Ensmust To Gene Symbol Using Mygene Module In Python

Question

[hicsuntdrac0nis]

I have a list of ensembl transcript IDs

ens = ['ENSMUST00000114694', 'ENSMUST00000028279', 'ENSMUST00000051301', 'ENSMUST00000038053', 'ENSMUST00000078988', 'ENSMUST00000115314', 'ENSMUST00000041124', 'ENSMUST00000022696', 'ENSMUST00000067689', 'ENSMUST00000162505', 'ENSMUST00000141755', 'ENSMUST00000111427', 'ENSMUST00000042868', 'ENSMUST00000160583', 'ENSMUST00000037182', 'ENSMUST00000131186']

I've downloaded and install mygene

import mygene

how do I convert these to the official gene symbol?

Answer 1

[Newgene]

It's easy to do that using mygene Python module:

import mygene
mg = mygene.MyGeneInfo()
mg.querymany(ens, scopes='ensembl.transcript')

That's it!

[Gjain]

Thanks... This works great.

import mygene
mg = mygene.MyGeneInfo()
ens = ['ENSG00000148795', 'ENSG00000165359', 'ENSG00000150676']
ginfo = mg.querymany(ens, scopes='ensembl.gene')

for g in ginfo:
 for k, v in g.iteritems():
  print "- {0: <10}: {1}".format(k, v)
 print 

### OUTPUT ###

- name      : cytochrome P450 family 17 subfamily A member 1
- symbol    : CYP17A1
- taxid     : 9606
- entrezgene: 1586
- query     : ENSG00000148795
- _id       : 1586

- name      : integrator complex subunit 6 like
- symbol    : INTS6L
- taxid     : 9606
- entrezgene: 203522
- query     : ENSG00000165359
- _id       : 203522

- name      : coiled-coil domain containing 83
- symbol    : CCDC83
- taxid     : 9606
- entrezgene: 220047
- query     : ENSG00000150676
- _id       : 220047

Answer 2

[GANI]

I don't think you can use Ensembl Transcript IDs with the mygene module.However you can use it with Ensembl Gene IDs. Following snippet shows a sample using Human gene identifiers

import mygene
mg = mygene.MyGeneInfo()
geneList = ['ENSG00000148795', 'ENSG00000165359', 'ENSG00000150676']
geneSyms = mg.querymany(geneList , scopes='ensembl.gene', fields='symbol', species='human')

Check the following Gist for more information

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

[hicsuntdrac0nis]

do you know of any way I can convert a list of transcript IDs into gene symbols ? I usually use biodbnet but my list is ~20k and it just freezes. biodb.jp isn't working for converting transcript IDs . I just need a way to convert these IDs .

Answer 3

[Emily]

No idea how to work mygene. I would recommend using the Perl API, which you can learn about using this online course.

[Chris Cole]

I agree. I always prefer to go via the ensembl API.

Alternative methods could be to use biomart or PyCogent: http://pycogent.org/

[Emily]

BioMart won't work for 20,000 IDs. It'll break down partway through your query, without warning, only giving you a partial dataset.

Answer 4

[Francesco]

Hello, for who needs a module in python I developed this library for who is looking for a python lightweight gene-id library conversion tool.

Answer 5

[Kermit]

Within the same ecosystem as mygene

from biothings_client import get_client
gene_client = get_client('gene')

gene_client.getgene('ENSG00000237801', fields='symbol')
"""
{'_id': 'ENSG00000237801', '_version': 1, 'symbol': 'AMD1P2'}
"""


gene_client.getgenes(['ENSG00000237801', 'ENSG00000210195'], fields='symbol')
"""
[
    {'query': 'ENSG00000237801', '_id': 'ENSG00000237801','_version': 1,'symbol': 'AMD1P2'},
    {'query': 'ENSG00000210195', '_id': '4576', '_version': 1, 'symbol': 'TRNT'}
]
"""