[Genome] refseq table question

[Brooke Rhead]

Hello again Jennifer,

You might find the 'name' field of the 'description' table useful.  It 
contains the information from the DEFINITION line in the GenBank record. 
  For instance, for GABRA3 (NM_000808)
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=156602646
the DEFINITION line contains the text "Homo sapiens gamma-aminobutyric 
acid (GABA) A receptor, alpha 3 (GABRA3), mRNA."

The 'refGene' table is connected to the 'gbCdnaInfo' table, which is 
then linked to the 'description' table, like so:

hg18.gbCdnaInfo.acc (via refGene.name)
hg18.description.id (via gbCdnaInfo.description)

You can use the "selected fields from primary and related tables" output 
format in the Table Browser to connect the fields from the refGene table 
to the description table.

You might also find the 'product' field of the 'refLink' table useful. 
It contains the description of the protein product from the GenBank 
record (in the "FEATURES" section, under "CDS", then "/product").  The 
text in this field for GABRA3 is "gamma-aminobutyric acid A receptor, 
alpha 3 precursor".

Perhaps one of these fields is what you are looking for.

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Brooke Rhead wrote:
> Hi Jennifer,
> 
> Can you be more specific about what you mean by "actual name of the 
> gene", and maybe give an example or two?  Do we display it anywhere on 
> our site?  I'm trying to figure out if this is something we store in a 
> table here that I could point you to.
> 
> --
> Brooke Rhead
> UCSC Genome Bioinformatics Group
> 
> 
> Barb, Jennifer (NIH/CIT) [E] wrote:
>> 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
>>> http://www.soe.ucsc.edu/mailman/listinfo/genome
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome