[Genome] refseq table question

[Barb, Jennifer (NIH/CIT) [E]]

Hi Brooke,
Thank you, that is helpful although I was actually looking for the
actual name of the gene and not just the gene symbol and id.  Perhaps
there is no way to obtain that directly from UCSC and I would have to go
to NCBI and download Refseq and parse that for the information that I am
looking for?  What do you think?
Jennifer

 
 
-----Original Message-----
From: Brooke Rhead [mailto:rhead at soe.ucsc.edu] 
Sent: Monday, November 05, 2007 5:42 PM
To: Barb, Jennifer (NIH/CIT) [E]
Cc: genome at soe.ucsc.edu
Subject: Re: [Genome] refseq table question

Hello Jennifer,

The 'refGene' table contains a 'name' field, which corresponds to the 
transcript ID, and a 'name2' field, which corresponds to the gene ID. 
You can use the Table Browser to get this information.

Configure the Table Browser with the clade, genome, and assembly of 
interest.  Then select:

group: Genes and gene prediction tracks
track: RefSeq Genes
table: refGene
region: genome
output format: selected fields from primary and related tables

Hit "get output", then select the boxes next to "name" and "name2".  Hit

"get output" again.

You should see two columns corresponding to the transcript ID and gene 
name.  For example, the first several results from this Table Browser 
query (using the human, March 2006 assembly) look like this:

#name	name2
NM_024763	WDR78
NM_207014	WDR78
NM_145243	OMA1
NM_012102	RERE
NM_024503	HIVEP3
NM_001042682	RERE
NM_001042681	RERE
...

I hope this information helps.  If this is not what you were looking 
for, or if we can clarify any of the above, please feel free to write 
back to this mailing list.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



Barb, Jennifer (NIH/CIT) [E] wrote:
> I am trying to obtain the refseq gene names along with the transcript
id
> number from the Refseq table from the UCSC genome browser website but
I
> only seem to find either a transcript id or a gene symbol, but no gene
> names/titles.  Does anyone have a way to pull this info out of the
> tables on the website?
> Sincerely,
> Jennifer
> 
>  
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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