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

Mike Cherry cherry at stanford.edu
Wed Jun 6 09:50:11 PDT 2012


Uniprot annotates proteins. Proteins have the function. Non-coding would be found with other IDs if they have been annotated by others. 

Gene Ontology annotated the gene product the entity with function. Nonetheless other IDs should be available for searching. 

-Mike. typos by iPhone. 

On Jun 6, 2012, at 9:07 AM, Christian Cole <C.Cole at dundee.ac.uk> wrote:

> Hi Mike,
> 
> OK. So that answers my original question regarding confusion over ensembl
> IDs, which, to recap, was why do the AmiGO docs mention Ensembl, but then
> is not available as an option in the term enrichment tool.
> 
> So UniProt IDs are preferred for searching in GO, correct? If so, is it
> just me who finds it strange that /protein/ IDs are used to find /gene/
> ontology terms? Are non-coding genes excluded from GO.
> Cheers,
> 
> 
> Chris
> 
> On 05/06/2012 22:46, "Mike Cherry" <cherry at stanford.edu> wrote:
> 
>> Chris,
>> 
>> Ensembl IDs are not in the GO database.  I think that is the issue here.
>> If you use http://www.uniprot.org/mapping/ to convert them all to
>> UniProtKB AC you will find the annotations.
>> 
>> The GO annotations for human are provided by UniProt.
>> 
>> -Mike
>> 
>> 
>> 
>> On Jun 5, 2012, at 1:45 PM, Christian Cole wrote:
>> 
>>> Hi Rama,
>>> 
>>> I don't understand why they're not in the GO database. For example the
>>> first gene, FLG, has several annotations in GOA:
>>> http://www.ebi.ac.uk/QuickGO/GProtein?ac=P20930
>>> 
>>> Where's the disconnect?
>>> Cheers,
>>> 
>>> Chris
>>> 
>>> 
>>> 
>>> On 5 Jun 2012, at 20:21, "Rama Balakrishnan" <ramab at stanford.edu> wrote:
>>> 
>>>> HI Christian,
>>>> 
>>>> The IDs aren't in the GO Database meaning they don't have a GO
>>>> annotation and hence did not make it to the GO database. It will be
>>>> wonderful if you can send us some papers for some of these very well
>>>> characterized genes. Once we curate them, they should be available in
>>>> the GO Database and for your analysis. Hope this answers your question.
>>>> 
>>>> Best,
>>>> 
>>>> Rama
>>>> 
>>>> On Jun 5, 2012, at 1:16 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
>>>>> 
>>>> 
>>>> 
>>> 
>>> 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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