[ensembl-dev] probe annotations

[njohnson at ebi.ac.uk]

Hi Koray

This is quite an old DB, but I guess you use this to access NCBI36
assembly. The array data was not officially migrated to the funcgen DB
until a later release, so you need to be looking at the core DB for this
info.

Nath

> I try to use mysql server of EBI...
>
> the db:
> homo_sapiens_funcgen_48_36j
>
> tried to call transcript id with probeset id:
> mysql> select * from xref where external_db_id=3102 limit 5;
> +---------+----------------+---------------+---------------+---------+-------------+-----------+--------------------------+
> | xref_id | external_db_id | dbprimary_acc | display_label | version |
> description | info_type | info_text |
> +---------+----------------+---------------+---------------+---------+-------------+-----------+--------------------------+
> | 2304380 | 3102 | 216412_x_at | 216412_x_at | 1 |
> NULL | MISC | probeset_size 11 hits 6 |
> | 2304439 | 3102 | 206171_at | 206171_at | 1 |
> NULL | MISC | probeset_size 11 hits 11 |
> | 2304559 | 3102 | 214226_at | 214226_at | 1 |
> NULL | MISC | probeset_size 11 hits 10 |
> | 2304368 | 3102 | 212997_s_at | 212997_s_at | 1 |
> NULL | MISC | probeset_size 11 hits 6 |
> | 2304361 | 3102 | 208488_s_at | 208488_s_at | 1 |
> NULL | MISC | probeset_size 11 hits 8 |
> +---------+----------------+---------------+---------------+---------+-------------+-----------+--------------------------+
>
> How can i combine xref_id to transcript_d?
> This did not work for example:
>
> mysql> select gene_id from transcript where display_xref_id=2304439;
> Empty set (0.08 sec)
>
>
>
> ----- Original Message -----
> From: njohnson at ebi.ac.uk
> Sent: 12/02/10 09:58 AM
> To: Koray Doðan Kaya
> Subject: Re: [ensembl-dev] probe annotations
>
> Hi
>
> The info you need is detailed in the following example script:
>
> ensembl-functgenomics/scripts/examples/microarray_annotation_example.pl
>
> This info is stored in the xref schema of the funcgen db i.e the xref,
> object_xref and external_db tables.
>
> I'm not sure what you mean by live matching.
>
> Nath
>
>
>> Hi Folk,
>>
>> It is well known that ENSEMBL already aligned each probeset to each
>> transcript. It is easy to go from gene to any probeset id in any array
>> platform via PERL API. I wanna ask the reverse, if my input is a probe
>> set
>> id or probe id is there a quick way of reaching to the gene? Are there
>> any
>> pre defined tables queryble via sql for this purpose? Or did anybody
>> write
>> a script about it? I dont want to use the biomaRt web site because it
>> needs to use hands. I need live matching by the way..
>>
>>
>> Thanks..
>>
>>
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>>
>