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[go-helpdesk] [go-software] Fwd: Term enrichment tool

Seth Carbon sjcarbon at lbl.gov
Fri Jun 1 13:32:13 PDT 2012


Christian/Rama,

In summary, the data does not appear to be in the database.

Specifically, when trying these out against recentish databases, out of
the fourteen, eleven were found. All of them were from "GermOnline", and
none of them joined with gene_product or evidence.

Cheers,

-Seth


On 06/01/2012 11:58 AM, Rama Balakrishnan wrote:
> Hi Christian,
> 
> Sorry for the delay in responding. I am not sure why these IDs don't
> work. I have cc'd the software group on this email. You will hear from
> them soon.
> 
> Best,
> Rama
> 
> 
> Begin forwarded message:
> 
>> *From: *Christian Cole <C.Cole at dundee.ac.uk <mailto:C.Cole at dundee.ac.uk>>
>> *Date: *May 28, 2012 1:25:29 AM PDT
>> *To: *Rama Balakrishnan <ramab at stanford.edu <mailto:ramab at stanford.edu>>
>> *Subject: **Re: Term enrichment tool*
>>
>> Hi Rama,
>>
>> Thanks for the reply. These are some of the IDs used. I don't think it's
>> an issue of missing GO annotations as other tools do find matches.
>>
>>
>>
>>
>>  ENSG00000143631
>>  FLG
>>
>>
>>  ENSG00000138615
>>  CILP
>>
>>
>>  ENSG00000163220
>>  S100A9
>>
>>
>>  ENSG00000120885
>>  CLU
>>
>>
>>  ENSG00000173918
>>  C1QTNF1
>>
>>
>>  ENSG00000163993
>>  S100P
>>
>>
>>  ENSG00000166780
>>  C16orf45
>>
>>
>>  ENSG00000231079
>>  AC105402.4.1
>>
>>
>>  ENSG00000167779
>>  IGFBP6
>>
>>
>>  ENSG00000113758
>>  DBN1
>>
>>
>>  ENSG00000004776
>>  HSPB6
>>
>>
>>  ENSG00000135750
>>  KCNK1
>>
>>
>>  ENSG00000221857
>>  FXYD1
>>
>>
>>  ENSG00000172638
>>  EFEMP2
>>
>>
>> Best,
>>
>> Chris
>>
>>
>>
>> On 27/05/2012 21:53, "Rama Balakrishnan" <ramab at stanford.edu
>> <mailto:ramab at stanford.edu>> wrote:
>>
>>>
>>>
>>>
>>> Hi Chris,
>>>
>>>
>>> Thanks for writing in. Can you please send me your IDs (a small subset
>>> will do) so I can check where the problem is? It is possible that some of
>>> these IDs don't have GO annotations and hence are not in the GO database.
>>>
>>>
>>> Thanks,
>>>
>>>
>>> Rama
>>>
>>> On May 24, 2012, at 8:09 AM,
>>> go-helpdesk-bounces at lists.stanford.edu
>>> <mailto:go-helpdesk-bounces at lists.stanford.edu>
>>> <mailto:go-helpdesk-bounces at lists.stanford.edu> wrote:
>>>
>>>
>>>
>>> From:
>>> c.cole at dundee.ac.uk <mailto:c.cole at dundee.ac.uk>
>>>
>>> Date:
>>> May 24, 2012 5:34:09 AM PDT
>>>
>>> To:
>>> go-helpdesk at mailman.stanford.edu
>>> <mailto:go-helpdesk at mailman.stanford.edu>
>>>
>>> Subject:
>>> GO Help query (from website)
>>>
>>>
>>>
>>>
>>> Email: c.cole at dundee.ac.uk <mailto:c.cole at dundee.ac.uk>
>>> Name: Software (from Chris Cole)
>>> Text: Hi,
>>>
>>> I'm trying to use the Term Enrichment tool on the Amigo site, but it
>>> keeps complaining that it can't find my gene IDs. I've tried ensembl gene
>>> IDs plus HGNC symbols. Before, I try and convert them to something else,
>>> can you clarify which IDs Amigo works with?
>>> The documentation is unclear and inconsistent.
>>>
>>> An example of inconsistency is that the docs regarding database filtering
>>> makes reference to Ensembl, but Ensembl is not available as an option on
>>> the form.
>>> Many thanks,
>>>
>>> Chris
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>
>>
>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>
> 
> 
> 
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