[ensembl-dev] CpG Island

[Bert Overduin]

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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>
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-- 
Bert Overduin, Ph.D.
Vertebrate Genomics Team

EMBL - European Bioinformatics Institute
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD
United Kingdom

http://www.ebi.ac.uk/~bert

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