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[go-helpdesk] Fwd: Term enrichment tool

Rama Balakrishnan ramab at stanford.edu
Fri Jun 1 11:58:02 PDT 2012


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>
> Date: May 28, 2012 1:25:29 AM PDT
> To: Rama Balakrishnan <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> 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> wrote:
>> 
>> 
>> 
>> From:
>> c.cole at dundee.ac.uk
>> 
>> Date:
>> May 24, 2012 5:34:09 AM PDT
>> 
>> To:
>> go-helpdesk at mailman.stanford.edu
>> 
>> Subject:
>> GO Help query (from website)
>> 
>> 
>> 
>> 
>> Email: 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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