How to get KgXref (gene symbol) with the results when using ensGenes

[Mohamed Aburweis]

For human hg19 (GRCh37/2009), if I choose the Genes and Genes predication from group and ensGenes from track and selected fields from primary and related tables, how can I get KgXref

 (the gene symbol) with the results as using USCS genes as attached in the screenshots below. 

Also for other species like rat (rn50, cow Tau7), and chicken(galGal4) how I know which ensemble release number you used for them.

[Steve Heitner]

Hello, Mohamed.

You can get to the kgXref table in the Table Browser by adding linked tables, but I think the ensemblToGeneName table would be better in this case.  The kgXref table doesn’t have a corresponding entry for each item in the ensGene table, but ensemblToGeneName does.  To do this, perform the following steps:

1. Navigate to http://genome.ucsc.edu/cgi-bin/hgTables

2. Select the following options:
Clade: Mammal
Genome: Human
Assembly: Feb. 2009 (GRCh37/hg19)
Group: Genes and Gene Predictions
Track: Ensembl Genes
Output format: selected fields from primary and related tables

3. Click the “get output” button

4. In the “Linked Tables” section, check the “hg19.ensemblToGeneName” checkbox

5. Click the “allow selection from checked tables” button

6. In the “hg19.ensemblToGeneName fields” section, check the “value” checkbox

7. In the “Select Fields from hg19.ensGene” section, check whichever fields you would also like to include in your output

8. Click the “get output” button

To get the Ensembl Genes version number for other assemblies, just visit each Ensembl Genes description page and view the “Data version” line as with hg19.  For rn5 for example:

1. Navigate to http://genome.ucsc.edu/cgi-bin/hgGateway?db=rn5

2. Click the “submit” button

3. Scroll down to the track listings and in the “Genes and Gene Predictions” track group, click the “Ensembl Genes” link

4. View the “Data version” line at the top of the description page

Please contact us again at gen...@soe.ucsc.edu if you have any further questions.  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.

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Steve Heitner
UCSC Genome Bioinformatics Group

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