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

Seth Carbon sjcarbon at lbl.gov
Tue Jun 5 13:55:36 PDT 2012


Christian,

While I'm unable to comment on whether or not items should be in the
database and their sources, I'd like to give a more nuanced explanation
of how the term enrichment tool works in your case.

Some of your IDs do have traces in the GO database, but do not show up
during enrichment. Looking a little closer, it turns out that these IDs
are only found in the seq database cross-reference part of the database.
Given the volume of input and the amount of time that AmiGO has before
clients timeout, AmiGO cannot search all possible ways to resolve an
ID--if something cannot be quickly found, it is abandoned and the next
identifier is checked.

Given this, one way to possibly improve results would be to map your IDs
into a something else (like UniProtKB) and retry. A list of resources
for that is kept on our wiki:

  http://wiki.geneontology.org/index.php/Tools_ID_Mapping

Best wishes,

-Seth


On 06/05/2012 01:16 AM, Christian Cole wrote:
> Hi Seth,
> 
> 
> Thanks for the reply.
> 
> I understand that the IDs aren't in the database (which database?), but
> you don't comment on whether they *should* be? Some of the genes below are
> very well characterised (as are many many in my full list) and my feeling
> is that they should at least have some GO annotations.
> 
> Does this mean there's a problem with the database or something else?
> Cheers,
> 
> Chris
> 
> On 01/06/2012 21:32, "Seth Carbon" <sjcarbon at lbl.gov> wrote:
> 
>> 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
>>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> go-software mailing list
>>> go-software at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/go-software
>>
>>
> 
> 
> The University of Dundee is a registered Scottish Charity, No: SC015096
> 
> 
> 



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