[Genome] the coordinates of annotated genes in hg18

[Kayla Smith]

Jun,

You can download tables from our website by clicking on the downloads 
button the left-hand side of the main page.  Click on human --> hg18 --> 
annotation database.   Try the knownGene.txt.gz file.   You might also 
look at the refGene.txt.gz table

It sounds like you want to do some detailed intersections between your 
set of coordinates and the knownGene table.  I will point you in the 
direction of our Table Browser ("Tables" on the blue bar on the top of 
the main page), but you're going to come to a point where your results 
wont correlate which of your coordinates intersected with which gene. 
 From your message, that might not be important to you.

Using the Table Browser, you'll need to make a few custom tracks.

1.  A custom track of the introns only from knownGene
2.  A custom track of the exons only from knownGene
3.  A custom track of the introns+exons from knownGene (make this by 
combining the first two CTs) Note this is the same as simply making a 
custom track of the knownGenes as they are.
4.  A custom track of the complement of #3 for "everything else" (aka 
intergenic regions)
5.  A custom track of your 1000 coordinates

Once you have those custom tracks set up, you can intersect them in any 
way you like, to get the information you're looking for.

Here is the User's Guide for general information on creating Custom 
Tracks (CT): 
http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks


Some details.   I'll show you how to make a custom track of introns:

1a. Open the Table Browser
1b.  set the following options:
   clade: Vertebrate
   genome: Human
   assembly: Mar 2006
   group: Genes and Gene Prediction Tracks
   track:  Known Genes
   table: knownGene
   region: genome
   output format: custom track
     Click "get output"
1c.  On the next page, select the radio button for "introns", be sure to 
name this custom track appropriately, and press "get custom track in 
table browser."
1d.  You now have a custom track of the introns of the Known Genes.



Here's how to make a CT of the intergenic regions:
4a.  To combine the Introns and Exons, etc.  you can do the following:
4b.  set the following options:
   clade: Vertebrate
   genome: Human
   assembly: Mar 2006
   group: Custom Tracks
   track:  tb_knownGeneINTRONSONLY (this is what I named my CT)
   table: ct_tbknownGeneINTRONSONLY
   region: genome
   intersection: create
4c.    On the intersection page, pull down the menu to choose your exons 
track.  Choose a "base-pair-wise union [OR]"  Also select the checkboxes 
that complement the introns and the exons at the bottom of the page.
     click submit.
   output format: custom track
     Click "get output"
4d.  This should give you the intergenic regions.


5.  To make a custom track of your 1000 positions, you can use our 
custom track tool (this is outside of the table browser).  Go to the 
gateway page for hg18 and click on "manage custom tracks".


 From there you're own your own for how you want to manage your sets of 
results.

To make things a little easier on you (temporarily) I've created a 
session, which I'll give you access to.  This session has the tracks 
I've described above already created.  It will expire soon, however.

Here is the link to my session:
http://genome.cse.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=Kayla&hgS_otherUserSessionName=kayla%2Dhg18%2Dintrons%2Dand%2Dexons

Or you can go to the Session tool and type in my
name: Kayla
Session: kayla-hg18-introns-and-exons

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.











Jun Wang wrote:
> Hello,
>     I want to know the genetic context of a list of chromosomal  
> locations( about 1000) in hg18. For example, for chrX_71181096+442, I  
> want to know whether it is in the gene region or intergenetic region  
> or cross both gene and inter-genetic region, and further if it is in  
> a complete gene region, whether it is in the intronic  or exonic region.
>      Therefore, I want to compare the chromosomal coordinates of my  
> list locations with the chromosomal coordinates of annotated genes in  
> hg18. I am wondering whether I can find such those files including  
> the chromosomal coordinates of annotated genes in hg18 from you and  
> where I can find it. or Do you have any other suggestions?
> 
> Thanks a lot!
> Jun
> 
> 
> Jun Wang
> University of Chicago
> 1101 E. 57th ST.
> Chicago, IL, 60637
> 
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome