[Genome] Finding Entrez gene numbers in C. elegans browser

[Pauline Fujita]

Hello John,

You can get the data that you're looking for using the table browser 
found here:

   http://www.genome.ucsc.edu/cgi-bin/hgTables

Then select:

    clade: Nematode
    genome: C. elegans
    assembly: Jan. 2007
    group: Genes and Gene Prediction Tracks
    track: RefSeq Genes
    table: refGene
    region: genome
    output format: selected fields from primary and related tables

Then, when you click on "get output" it will take you to a menu where 
you can select which columns you want to appear in the output. In this 
particular case you would want to select:

    the "name" box in the upper table

then select from the "Linked Tables" section select:

    "refLink"

and click "Allow Selection From Checked Tables". Then in the next screen 
you will see a "ce4.refLink fields" section and from that select:

    "locusLinkId"

Entrez used to be called LocusLink so "locusLinkId" should be the Entrez 
ID. Then click "get output" again and you should get a text file with 
the data of interest. Hopefully this information was helpful and answers 
your question. If you have further questions or require clarification 
feel free to contact the mailing list at genome at soe.ucsc.edu.

Regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


Pace, John K wrote:
> I am trying to find the table that stores the Entrez gene numbers for
> the C. elegans Jan 2007 browser.  Here are the steps I am currently
> following:
>
>  
>
> Click on Genomes, select C. elegans, Jan. 2007.  The search term is
> "age-1".  It brings up the results screen and I click on the age-1
> RefSeq gene.  This takes me to the browser.  I click on the age-1 gene
> in the RefSeq track.  This takes me to the detail for the age-1 gene.
> The second entry on this detail screen reads  Entrez Gene:  174762.
>
>  
>
> I need to be able to query several thousand genes by the RefSeq gene
> name and get this Entrez Gene name, but I can't seem to find where the
> Entrez Gene information is stored.  Can you help?
>
>  
>
> Thanks,
>
>  
>
> John Pace
>
> Jpace at uta.edu
>
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