mapping isoform ID to ensembl

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Sridhar, Sriram

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Aug 2, 2016, 5:12:51 PM8/2/16
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Dear Sir or Madam,

 

I am working with isoform data from TCGA for a project. I am trying to map isoform IDs mapping to the human androgen receptor to their appropriate ensemble IDs. I used the table browser to map isoform IDs to gene symbols, but I’m not sure how to map to ensembl transcripts. Any input you might have on how to do this would be much appreciated.

 

Best regards,

Sri

 

Sriram Sridhar, PhD

Translational Bioinformatics

MedImmune

One MedImmune Way
Gaithersburg, MD 20878
301-398-6386 (office)
617-877-1485 (cell)
srid...@medimmune.com

 

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Cath Tyner

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Aug 2, 2016, 8:56:39 PM8/2/16
to Sridhar, Sriram, gen...@soe.ucsc.edu
Hello Sri,

Thank you for using the UCSC Genome Browser. Please try the instructions below to find corresponding ensembl IDs, and please reply to this list if you have further questions.

Go to Table Browser, and configure as:

Assembly =hg19 (for example)
Group = Genes and Gene Predictions
Track = UCSC Genes
Table = knownToEnsemb
Table = hgFixed.transMapGeneUcscGenes

identifiers: paste in IDs or upload list

e.g,
uc022bqo.2
uc004cor.1

Output format: selected fields from primary and related tables

Click "get output."

Next, under the first section, "Select fields from hg19.knownToEnsembl" click "name."

Then, scroll down to select (check the box for) the linked tabled, "hg19: esnGtp" and "hg19: kgXref."

Click the button at the bottom of the page, "allow selection from checked tables."

Under the section "hg19.ensGtp fields" click the fields for "gene" and "transcript."

Under the section "hg19.kgXref fields" click the fields for "geneSymbol."

Click the button at the top of the page, "get output."

Example output:

#hg19.knownToEnsembl.name hg19.ensGtp.gene hg19.ensGtp.transcript hg19.kgXref.geneSymbol
uc004cor.1 ENSG00000210077 ENST00000387342 DQ582265
uc022bqo.2 ENSG00000211459 ENST00000389680 JB137816

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Sridhar, Sriram

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Aug 3, 2016, 11:58:01 AM8/3/16
to Cath Tyner, gen...@soe.ucsc.edu

Hi Cath,

 

Thanks for the quick reply. I’m trying to configure the Table Browser as you’ve outlined, but I only see one table option:

 

I wonder if I’m missing something? I’m trying to figure out how to set the two table options you’ve outlined in your email. Thanks again for your help!

 

Sri

Cath Tyner

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Aug 3, 2016, 3:02:24 PM8/3/16
to Sridhar, Sriram, gen...@soe.ucsc.edu
Hello Sri,

My apologies; please ignore the line, "Table = hgFixed.transMapGeneUcscGenes" from the instructions. Here is a video of the correct steps: https://drive.google.com/file/d/0ByGov80wHkvuSms5SVZ5clcyWEE/view

Please respond to this list if you have further questions and our team will be happy to help.

Cath
. . .
Cath Tyner
UCSC Genome Browser, Software QA & User Support
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