[Genome] Question?

[Kayla Smith]

Luis,

For genes where you don't have the NM_ identifiers, you can use the 
kgXref table.  Select the following options in the Table Browser:

clade: Vertebrate
genome: Human
assembly: Mar. 2006
table: knownGene
region: genome
filter: create

On the filter page scroll down and select the box next to kgXref.  Then 
click on "Allow Filtering Using Fields in Checked Tables".   Under the 
header hg18.kgXref based filters, set:

geneSymbol "does match" TLR1  (you could try pasting in all your non NM_ 
names here)

click "submit"

Back in the Table Browser, toggle "output format" to "selected fields 
from primary and related tables"

click "get output"

Select the boxes: name, chrom, txStart, txEnd from hg18.knownGene and 
also the geneSymbol box from hg18.kgXref fields.

click "get output" one last time for your results.

I hope this is helpful to you.  Please don't hesitate to contact us 
again if you require further assistance.

Kayla Smith
UCSC Genome Bioinformatics Group



Luis Barreiro wrote:
> HI,
> 
> I have a simple question concerning the use of the Table Browser. 
> Indeed, I would need to have the gene transcript location in hg18 for 
> about 500 genes. I know how to get this information giving as gene 
> identifier in the format NM_XXX  (for example NM_003263) but since I 
> don't have this code for all my genes, I would like to obtain this 
> information using as gene identifier the HUGO nomenclature (e.g. TLR1 
> for the former example). Is it possible, and if so, how should I proceed?
> 
> Thanks a lot in advance
> Luis
> 
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