[Genome] help with a gene list

[Ann Zweig]

Hello Omid,

	You can obtain such a tab-delimited file by using the Table Browser on our 
website.  Press the "Tables" link in the blue navigation bar across the top of 
the browser window.  I will give you step-by-step instructions for the first
500,000 bases of chrX -- you can extrapolate from there.  We have several gene 
annotation tracks on the browser, I will explain how to use the Known Gene 
track, but if you want to use another track, you can change the 'track' and 
'table' selections in the instructions.

Configure the Table Browser like so:

genome: Human
assembly: Mar. 2006
group: Genes and Gene Prediction Tracks
track: Known Genes
table: knownGene
position: chrX:1-500000
output format: selected fields from primary and related tables

	Press "get output" button.  From this page, choose the fields from the 
knownGene table that you would like to view.  In your case: name, chrom, strand, 
either or both txStart/cdsStart, txEnd/cdsEnd.  This will provide you all of the 
information you asked for except "other aliases".

	To include other aliases, you will need to scroll down this page and click on 
the table named "kgXref".  This table includes other gene names such as 
SWISS=PROT, RefSeq, etc.  After checking the kgXref box, scroll to the bottom of 
the page and press the "Allow Selection From Checked Tables" button.  Now, in 
the hg18.kgXref section, select any other names you would like to see in your 
output.

	Depending on your selections, your output will look something like this:


#hg18.knownGene.name	hg18.knownGene.chrom	hg18.knownGene.strand 
hg18.knownGene.txStart	hg18.knownGene.txEnd	hg18.kgXref.mRNA	hg18.kgXref.spID 
hg18.kgXref.spDisplayID	hg18.kgXref.geneSymbol	hg18.kgXref.refseq

NM_018390	chrX	+	132991	160020	NM_018390	Q9NUJ7	Q9NUJ7_HUMAN	PLCXD1	NM_018390

NM_199326	chrX	-	214971	222590	NM_199326	Q96H01	Q96H01_HUMAN	PPP2R3B	NM_199326

NM_013239	chrX	-	214971	267627	BC063429,NM_013239,	Q9Y5P8,Q9Y5P8, 
2ACC_HUMAN,2ACC_HUMAN,	PPP2R3B,PPP2R3B,	
NM_013239,NM_013239,

BC063429	chrX	-	214975	267445	BC063429	Q96FD8	Q96FD8_HUMAN	PPP2R3B	NM_013239

BC063429	chrX	-	214975	267445	BC063429,NM_013239,	Q9Y5P8,Q9Y5P8, 
2ACC_HUMAN,2ACC_HUMAN,	PPP2R3B,PPP2R3B,	NM_013239,NM_013239,


	I hope this helps you get started using the UCSC Genome Browser.  Please don't 
hesitate to write back if you need more guidance.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu


omid gulban wrote:
> Hello All,
> 
> I am a new user of the UCSC genome browser system.
> 
> I would like to optain a tab-delimited file containing the following information from the most recent Human genome.
> 
> gene name
> other aliases
> chromosome
> start
> end
> strand
> 
> Thank You
> Omid
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome