canFam3.1 EnsembGeneID to GeneName

[Arumilli, Meharji]

Dear all,

We are trying to convert Ensembl Gene ID's to corresponding Gene Name for canFam3.1

The UCSC table for the "ensGene" track has the gene IDs and the transcript IDs but not the gene names.

ENSCAFG00000000001.3
ENSCAFG00000030108.1

And "ensemblToGeneName" table has the transcript ID with gene name. Would you help us how to match the Gene ID's retrieved from UCSC browser with the gene names?

Br
Mehar

[Cath Tyner]

Hello Mehar,

Thank you for your question regarding the joining of a field from a related table. There are two ways to achieve your goal, outlined below:

Option 1. 

If you have MySQL client libraries installed on your computer, you can connect to our public MySql database. 

https://genome.ucsc.edu/goldenPath/help/mysql.html

Below is a query which should provide output with gene IDs included:

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -N -e \

  'SELECT e.gene,e.transcript,e.protein,g.value FROM ensGtp e,

        ensemblToGeneName g

WHERE e.transcript = g.name' canFam3

Option 2. 

Alternatively, you can use our "Table Browser" tool (see our Table Browser User's Guide) by following these steps:

1. Navigate to "Tools > Table Browser" in the top horizontal blue menu bar

​ from our home page.​

2. Set your conditions:

Clade: Mammal
Genome: Dog
Assembly: canFam3.1
Group: Genes and Gene Prediction
Track: Ensembl Genes
Table: ensGene
Region: genome
Output format: selected fields from primary and related tables

3. Click "get output" to move to the next step.

4. Under the "Select Fields from canFam3.ensGene" section, check the "name2" checkbox.

5. Under the "Linked Tables" section, check the "canFam3.ensemblToGeneName" checkbox.

6. Click the button "Allow selection from linked tables."

7. In the "canFam3.ensemblToGeneName

​ ​

fields" section, check the "value" checkbox.

8. Click "get output."

You should now be able to view your output of Ensembl gene IDs and corresponding gene names for canFam3.1

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

​Enjoy,​

Cath
. . .

Cath Tyner

UC Santa Cruz Genomics Institute

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