[Genome] problem on mouse genome for promoter region prediction

[Brooke Rhead]

Hello Xu Jerry,

Here is a similar previously-answered question:

http://www.soe.ucsc.edu/pipermail/genome/2007-November/014963.html

(This is specific to TFBS, but you could also use the liftOver utility 
for the Eponine TSS or FirstEF tracks.  However, please see my note 
below about using liftOver -- you might want to use pslMap instead.)

Alternatively, you could intersect one of the human promoter tracks with 
the human Conservation track to get the corresponding mouse regions, as 
described in this answer:

http://www.soe.ucsc.edu/pipermail/genome/2007-June/013989.html

(Note that multiz17way has been replaced by multiz28way in hg18.  Also, 
there is another tool run by Penn State University called Galaxy that is 
very useful for working with MAF data, located here: 
http://main.g2.bx.psu.edu/ -- look under the "Fetch Alignments" tool on 
the left-hand side of the page.)

In either case, you could make a custom track in the mouse browser and 
intersect it with the mouse regions you found.

Another option would be to go in the opposite direction: use your 
compiled list of mouse coordinates to create a custom track in the human 
browser (either using liftOver, pslMap or the Conservation track to 
convert to human coordinates), then intersect that with one of the 
promoter tracks on the human browser.


NOTE about using liftOver:

liftOver is fairly coarse (just maps start and end), which makes it more 
useful for same-species mapping than cross-species mapping.  The program 
pslMap is much more detailed (it breaks the mapping down to the 
chainLink/gapless-block level), so it is better than liftOver for 
mapping gene-sized regions.

The pslMap program is available in our source tree, which is free for 
academic, nonprofit and personal use:
http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads

Typical pslMap options for running with one of our .over.chain files 
(for example, converting mm8 to hg18 coordinates) are:

pslMap -chainMapFile -swapMap mm8.input.psl mm8ToHg18.over.chain.gz 
hg18.output.psl

Note that the input to pslMap needs to be in PSL format, described here: 
http://genome.ucsc.edu/FAQ/FAQformat#format2 .  If you already have 
coordinates in BED format, our program genePredToPsl -bedFormat can be used.

The output of pslMap can be uploaded as a custom track, and/or 
translated back into BED format using the program pslToBed.

I hope this information is helpful.  If you have further questions, 
please feel free to contact us again at the genome mailing list address.

-- 
Brooke Rhead
UCSC Genome Bioinformatics Group


xu_jianzhen wrote:
> hi,genome
>   I am a member of GIBH,Chinese Academy of Science. I have compiled a lists of mouse (mm8) genome coordinates.I'd like to 
> use some predicton tools to search those regions to see whether they are promoter regions(or there are transcription start sites among them).
> In human genome, there are tracks of pre-computed predicted promoter region(human Mar.2006,for example:Eponine TSS or FirstEF),But 
> I can find one for mouse genome.Could you help me to solve this problem?
>  
>  
>  
>  
> Xu Jerry
> GIBH,CAS
>  
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
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