[ensembl-dev] CpG Island

[Susan Fairley]

Hi Yuan,

The process by which the score is generated is similar to the one 
described below although, as Bert mentioned, the minimum length 
requirement is 400bp. I believe the score reported is the maximum score 
reached for the island.

 From https://lists.soe.ucsc.edu/pipermail/genome/2004-July/005149.html:
"Instead of a sliding-window search for CpG islands, this cpg program
uses a running-sum score where a 'C' followed by a 'G' increases the
score by 17 and anything else decreases the score by 1.  When the
score transitions from positive to 0 (and at the end of the sequence),
the sequence in the current span is evaluated to see if it qualifies
as a CpG island (>200 bp length, >50% GC, >0.6 ratio of observed CpG
to expected)."

I hope that helps.

Regards,
Susan.

Bert Overduin wrote:
> Yuan,
> 
> Also note that for human Ensembl uses for CpG islands a cut-off of 400
> bp. Smaller CpG islands are not stored.
> 
> Cheers,
> Bert
> 
> On Wed, Jan 11, 2012 at 9:41 AM, Yuan Chen <yuan at sanger.ac.uk> wrote:
>> Thank very much, Susan.
>>
>> In the simple_feature table for cpg, there is score column, the maximum score is 34968 and minimum score is 37, do you know the meaning of this score ?
>>
>> yuan
>> On 11 Jan 2012, at 09:28, Susan Fairley wrote:
>>
>>> Hi Yuan,
>>>
>>> The CpG islands are stored as simple features in the human core database. Their analysis has the logic_name cpg.
>>>
>>> homo_sapiens_core_65_37 >select logic_name , count(*) from analysis, simple_feature where analysis.analysis_id =simple_feature.analysis_id group by logic_name ;
>>> +------------+----------+
>>> | logic_name | count(*) |
>>> +------------+----------+
>>> | cpg        |    23511 |
>>> | eponine    |    62774 |
>>> | firstef    |    89002 |
>>> | trnascan   |      834 |
>>> +------------+----------+
>>> 4 rows in set (0.36 sec)
>>>
>>> Kind regards,
>>> Susan.
>>>
>>> Yuan Chen wrote:
>>>> Hi All,
>>>> Do ENSEMBL have CpG island data on human available some where ?  Cheers
>>>> yuan
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> 
> 
>