[Genome] [Fwd: question UCSC Tables]

[Katleen De Preter]

Hello,

As I have understood well from your answer, it is not possible to get 
the original search terms in the output table. As this is a mixture of 
HUGO and Alias and some other types of identifiers, it would be very 
helpful to check for which of the input terms Genome Browser has found a 
match...

Best regards,

Katleen De Preter


Brooke Rhead schreef:
> Hello Kathleen,
>
> Are you by any chance using the "UCSC Genes" track or the "RefSeq 
> Genes" track?  Both of these tracks have some extra functionality in 
> the Table Browser that allow you to use an identifier that is NOT the 
> main identifier in the table you have selected.
>
> To see what I am referring to, look at the text at the top of the page 
> when you hit the "paste list" button.  For UCSC Genes, the text at the 
> top is:
>
> "Please paste in the identifiers you want to include. The items must 
> be values of the name field of the currently selected table, 
> knownGene, or the alias field of the alias table kgAlias."
>
> What is happening when you paste in HUGO identifiers is that the Table 
> Browser is going through the kgAlias table to make selections from the 
> knownGene table, but only the fields from the knownGene table are 
> returned.
>
> To include information from the kgAlias table in your output, choose 
> the output format "selected fields from primary and related tables".  
> Now hit "get output", and then from the Linked Tables section, check 
> the box for the kgAlias table and hit the "allow selection from 
> checked tables" button at the bottom of the page.  Be sure the 
> kgAlias.alias field is selected (as well as the fields you want to 
> retrieve from knownGene), and then hit "get output".
>
> You should see a new column on the end of your output that contains 
> the alias field from kgAlias.  Note that since one UCSC Gene ID 
> generally corresponds to several aliases, there are several names 
> listed in that column.  The identifier you originally entered should 
> be included in the list.
>
> I hope this information is helpful.  If you have further questions, 
> please do not hesitate to contact us again.  However, please send 
> future questions to genome at soe.ucsc.edu, our moderated forum for user 
> questions and support.  (Note that this is a public mailing list, see 
> http://genome.ucsc.edu/contacts.html for details.)
>
> -- 
> Brooke Rhead
> UCSC Genome Bioinformatics Group
>
>
>> -------- Original Message --------
>> Subject:     question UCSC Tables
>> Date:     Mon, 10 Dec 2007 17:29:16 +0100
>> From:     Katleen De Preter <Katleen.DePreter at ugent.be>
>> To:     cbseweb at cbse.ucsc.edu
>>
>>
>>
>> Dear Mr/Mrs,
>>
>> I would like to search the positions of a list of gene symbols (HUGO 
>> names and aliases). When I perform a search using the Tables 
>> function, I get a large list of results. However, in this results 
>> file, I cannot find the original Gene Symbols I have searched for. 
>> How can I obtain also the original list in the output file?
>>
>> Thank you in advance,
>> Best regards,
>>
>> Katleen De Preter

-- 
dr. ir. Katleen De Preter
Center for Medical Genetics Ghent (CMGG) 
Ghent University Hospital 
Medical Research Building (MRB), 2nd floor, room 120.038 
De Pintelaan 185, B-9000 Ghent, Belgium 
+32 9 332 5533 (phone) | +32 9 332 6549 (fax)

http://medgen.ugent.be 
Katleen.DePreter at UGent.be