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

Rama Balakrishnan ramab at stanford.edu
Thu Jun 7 13:26:44 PDT 2012


HI Christian,

I am glad you were able to map your IDs and you have it working.

Best,

Rama


Begin forwarded message:

> From: Christian Cole <C.Cole at dundee.ac.uk>
> Date: June 7, 2012 1:18:29 AM PDT
> To: Rama Balakrishnan <ramab at stanford.edu>
> Subject: Re: [go-software] Fwd: Term enrichment tool
> 
> Hi Rama,
> 
> Thanks. I see that now and have got it working with Uniprot IDs.
> 
> Thanks again for your perseverance.
> 
> Chris
> 
> 
> 
> 
> On 06/06/2012 22:31, "Rama Balakrishnan" <ramab at stanford.edu> wrote:
> 
>> 
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>> Hi Christian,
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>> Sorry for all the back and forth. Bottom line is you need to map your
>> Ensemble IDs to UniProt IDs to work with Term Enrichment.
>> http://wiki.geneontology.org/index.php/Tools_ID_Mapping
>> 
>> Here is why:
>> 
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>> It is true that GO annotations for FLG gene is pulled up when you search
>> on QuickGO or AmiGO for the ENSEMBL ID-ENST00000368799
>> <http://www.ensembl.org/id/ENST00000368799>.
>> ENSEMBL IDs are external accessions (not primary) in the GO database and
>> AmiGO is able to map the ENSEMBL ID to FLG by doing different db joins.
>> And this is easier to do when you are looking at just one gene.
>> But with Term Enrichment, when you have lot of genes with external IDs,
>> if the query is trying to resolve the IDs by doing joins, it takes a
>> while and hence that feature was disabled for Term enrichment.
>> 
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>> For these reasons you should map your gene IDs to UniProt IDs and then
>> try Term Enrichment.
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>> I apologize again for the delay in sorting this out. Please let me know
>> if you have any questions.
>> 
>> 
>> Best,
>> 
>> 
>> Rama
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>> 
>> 
>> On Jun 6, 2012, at 9:50 AM, Mike Cherry wrote:
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>> Uniprot annotates proteins. Proteins have the function. Non-coding would
>> be found with other IDs if they have been annotated by others.
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>> Gene Ontology annotated the gene product the entity with function.
>> Nonetheless other IDs should be available for searching.
>> 
>> 
>> -Mike. typos by iPhone.
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>> On Jun 6, 2012, at 9:07 AM, Christian Cole <C.Cole at dundee.ac.uk> wrote:
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>> Hi Mike,
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>> OK. So that answers my original question regarding confusion over ensembl
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>> IDs, which, to recap, was why do the AmiGO docs mention Ensembl, but then
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>> is not available as an option in the term enrichment tool.
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>> So UniProt IDs are preferred for searching in GO, correct? If so, is it
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>> just me who finds it strange that /protein/ IDs are used to find /gene/
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>> ontology terms? Are non-coding genes excluded from GO.
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>> Cheers,
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>> Chris
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>> On 05/06/2012 22:46, "Mike Cherry" <cherry at stanford.edu> wrote:
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>> Chris,
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>> Ensembl IDs are not in the GO database.  I think that is the issue here.
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>> If you use http://www.uniprot.org/mapping/ to convert them all to
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>> UniProtKB AC you will find the annotations.
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>> The GO annotations for human are provided by UniProt.
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>> -Mike
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>> On Jun 5, 2012, at 1:45 PM, Christian Cole wrote:
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>> Hi Rama,
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>> I don't understand why they're not in the GO database. For example the
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>> first gene, FLG, has several annotations in GOA:
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>> http://www.ebi.ac.uk/QuickGO/GProtein?ac=P20930
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>> Where's the disconnect?
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>> Cheers,
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>> Chris
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>> On 5 Jun 2012, at 20:21, "Rama Balakrishnan" <ramab at stanford.edu> wrote:
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>> HI Christian,
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>> The IDs aren't in the GO Database meaning they don't have a GO
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>> annotation and hence did not make it to the GO database. It will be
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>> wonderful if you can send us some papers for some of these very well
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>> characterized genes. Once we curate them, they should be available in
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>> the GO Database and for your analysis. Hope this answers your question.
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>> Best,
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>> Rama
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>> On Jun 5, 2012, at 1:16 AM, Christian Cole wrote:
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>> Hi Seth,
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>> Thanks for the reply.
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>> I understand that the IDs aren't in the database (which database?),
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>> but
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>> you don't comment on whether they *should* be? Some of the genes
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>> below are
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>> very well characterised (as are many many in my full list) and my
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>> feeling
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>> is that they should at least have some GO annotations.
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>> Does this mean there's a problem with the database or something else?
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>> Cheers,
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>> On 01/06/2012 21:32, "Seth Carbon" <sjcarbon at lbl.gov> wrote:
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>> Christian/Rama,
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>> In summary, the data does not appear to be in the database.
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>> Specifically, when trying these out against recentish databases, out
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>> of
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>> the fourteen, eleven were found. All of them were from "GermOnline",
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>> and
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>> none of them joined with gene_product or evidence.
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>> Cheers,
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>> -Seth
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>> On 06/01/2012 11:58 AM, Rama Balakrishnan wrote:
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>> Hi Christian,
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>> Sorry for the delay in responding. I am not sure why these IDs don't
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>> work. I have cc'd the software group on this email. You will hear
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>> from
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>> them soon.
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>> Best,
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>> Rama
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>> Begin forwarded message:
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>> *From: *Christian Cole <C.Cole at dundee.ac.uk
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>> <mailto:C.Cole at dundee.ac.uk>>
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>> *Date: *May 28, 2012 1:25:29 AM PDT
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>> *To: *Rama Balakrishnan <ramab at stanford.edu
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>> <mailto:ramab at stanford.edu>>
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>> *Subject: **Re: Term enrichment tool*
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>> Hi Rama,
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>> Thanks for the reply. These are some of the IDs used. I don't think
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>> it's
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>> an issue of missing GO annotations as other tools do find matches.
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>> ENSG00000135750
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>> KCNK1
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>> ENSG00000221857
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>> FXYD1
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>> ENSG00000172638
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>> Best,
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>> On 27/05/2012 21:53, "Rama Balakrishnan" <ramab at stanford.edu
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>> <mailto:ramab at stanford.edu>> wrote:
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>> Hi Chris,
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>> Thanks for writing in. Can you please send me your IDs (a small
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>> will do) so I can check where the problem is? It is possible that
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>> these IDs don't have GO annotations and hence are not in the GO
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>> database.
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>> Thanks,
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>> Rama
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>> On May 24, 2012, at 8:09 AM,
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>> go-helpdesk-bounces at lists.stanford.edu
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>> <mailto:go-helpdesk-bounces at lists.stanford.edu>
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>> <mailto:go-helpdesk-bounces at lists.stanford.edu> wrote:
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>> From:
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>> c.cole at dundee.ac.uk <mailto:c.cole at dundee.ac.uk>
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>> Date:
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>> May 24, 2012 5:34:09 AM PDT
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>> To:
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>> go-helpdesk at mailman.stanford.edu
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>> <mailto:go-helpdesk at mailman.stanford.edu>
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>> Subject:
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>> GO Help query (from website)
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>> Email: c.cole at dundee.ac.uk <mailto:c.cole at dundee.ac.uk>
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>> Name: Software (from Chris Cole)
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>> Text: Hi,
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>> I'm trying to use the Term Enrichment tool on the Amigo site, but
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>> it
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>> keeps complaining that it can't find my gene IDs. I've tried
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>> ensembl
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>> gene
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>> IDs plus HGNC symbols. Before, I try and convert them to something
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>> else,
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>> can you clarify which IDs Amigo works with?
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>> The documentation is unclear and inconsistent.
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>> An example of inconsistency is that the docs regarding database
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>> filtering
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>> makes reference to Ensembl, but Ensembl is not available as an
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>> option
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>> on
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>> the form.
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>> Many thanks,
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>> The University of Dundee is a registered Scottish Charity, No:
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>> SC015096
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>> _______________________________________________
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>> go-software mailing list
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>> go-software at lists.stanford.edu
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>> https://mailman.stanford.edu/mailman/listinfo/go-software
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>> The University of Dundee is a registered Scottish Charity, No:
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>> SC015096
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>> The University of Dundee is a registered Scottish Charity, No: SC015096
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>> _______________________________________________
>> 
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>> go-software mailing list
>> 
>> 
>> 
>> 
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>> 
>> 
>> go-software at lists.stanford.edu
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>> https://mailman.stanford.edu/mailman/listinfo/go-software
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>> The University of Dundee is a registered Scottish Charity, No: SC015096
>> 
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>> 
> 
> 
> The University of Dundee is a registered Scottish Charity, No: SC015096
> 

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