Hi Mahesh,
There are many methods of identifying CpG islands, and our method for
the CpG Islands track is fairly strict. This is from the methods section
of the track description page
(http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=cpgIslandExt):
"CpG islands were predicted by searching the sequence one base at a
time, scoring each dinucleotide (+17 for CG and -1 for others) and
identifying maximally scoring segments. Each segment was then evaluated
for the following criteria:
* GC content of 50% or greater
* length greater than 200 bp
* ratio greater than 0.6 of observed number of CG dinucleotides to
the expected number on the basis of the number of Gs and Cs in the
segment"
This previously answered question also has some additional information
about the criteria used:
https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-September/002087.html
We also have additional information on our genomewiki:
http://genomewiki.cse.ucsc.edu/index.php/CpG_Islands
Please don't hesitate to contact the mail list again if you have any
further questions.
Katrina Learned
UCSC Genome Bioinformatics Group
Mohan, Mahesh wrote, On 03/03/11 21:12:
> Dear Sir/Madam:
>
> I have been trying to identify a CpG island sequence in the promoter of the
> TCF4 gene in the human and rhesus. From the genome browser I was able to
> download a small CpG island sequence of about 291 bases long with ~30-32 CpG
> dinucleotides in the human and macaque. However, I did find a paper published
> last year looking at CpG methylation of the TCF4 promoter sequence in gastric
> carcinoma patients and where the authors had identified a CpG island sequence
> immmediately upstream of the transcription start site and have their enitre
> study on this sequence. However, I was surprised to find this CpG sequence
> missing in the genome browser sequence. I have attached a copy of the paper
> for your reference. I am wondering if you have strict criteria for defining a
> CpG island.
>
> Will look forward to hear your response.
>
>
> Thanks
> Mahehs
>
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