[Genome] CpG islands and TSS

[Brooke Rhead]

Hello Ilya,

Information on CpG islands is in the table 'cpgIslandExt', which is 
available from the Table Browser (hit the "Tables" link in the blue bar 
at the top of the page and look under the Expression and Regulation 
group for the CpG Islands track), or from the downloads page:
http://hgdownload.cse.ucsc.edu/downloads.html (go to the appropriate 
assembly, and then click the "annotation database" link and look for the 
  file 'cpgIslandExt.txt.gz').

The island length is in the 'length' field of the table, the field 
'perCg' contains the percentage of the island that is C or G (and the 
field 'numCg' contains the count of C and G in the island), and the 
observed/expected ratio is in the field 'obsExp'.

Finding the distance to the nearest transcription start site will be 
more difficult.  Depending on the assembly you are using, there may or 
may not be a TSS track available.  If there is, you will need to use 
your own tools to find the nearest TSS to a CpG Island and to calculate 
the distance between them.  There might be a tool at the Galaxy web site 
(http://main.g2.bx.psu.edu/ ; this site is run by Penn State) that might 
be useful for this.

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

--
Brooke Rhead
UCSC Genome Bioinformatics Group


Ioschikhes, Ilya wrote:
> Hello,
>  
> Please let me know how could I get following information for known CpG
> islands:
>  
> Length;    C,G content;   Observed/Expected CpG ratio;   Distance from
> nearest TSS.
>  
> Thanks,
>  
> 
> Ilya Ioshikhes, Ph.D.
> 
> Assistant Professor
> 
> Department of Biomedical Informatics and
> 
> Department of Molecular & Cellular Biochemistry,
> 
> Associate Investigator 
> 
> Davis Heart and Lung Research Institute,
> Ohio State University
> 3172c Graves Hall
> 333 W. 10th Ave.
> Columbus, OH 43210
> TEL: +1 (614) 292-8929
> Fax: +1 (614) 688-6600
> E-mail: Ilya.Ioschikhes at osumc.edu <mailto:Ilya.Ioschikhes at osumc.edu> 
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome