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[SO-devel] Re: annotating to pseudogenes

Karen Eilbeck eilbeck at fruitfly.org
Tue Mar 14 10:29:19 PST 2006


I am late diving in on this because my mail is behaving badly and 64  
messages about pseudogenes arrived at once.

In SO, pseudogenes have no function. If they do, they must be annotated  
as the thing they are ie some kind of ncRNA

There is a relationship between pseudogene and its functional homolog (  
a gene) called for the want of a better term  
'non_functional_homolog_of'.

This way you can infer the function the pseudogene would have had if  
was a live gene. (Assuming that your genes are annotated with SO and GO  
of course!)

SO is trying to capture what regions of sequence are now as we annotate  
them not what they were or will be.

--Karen

On Mar 14, 2006, at 10:57 AM, Pankaj Jaiswal wrote:

> I think the best way to handle this is to effectively use the  
> object_type field in the association files. Instead of using just the  
> object_type 'gene' by default, try diversifying by using the types  
> such as
> pseudogene/transcript/peptide/mi-RNA/etc.
>
> Pankaj
>
> Matthew Berriman wrote:
>
>> the key thing here is that they are not necessarily decayed genes.   
>> They are "stored" in an inactive form, so that they can be assembled  
>> by gene conversion etc into "functional" genes when transcribed.   
>> They do, therefore, indirectly encode gene products.  I would argue  
>> that in this case, they do indirectly have a function and should  
>> receive some kind of GO annotation. A pragmatic consideration is that  
>> >10% of the genome is dedicated to evading the mammalian immune  
>> system and that this should be annotated.  Unfortunately, the  
>> situation is complicated by the fact that amongst the large  
>> repertoire of "functional" pseudogenes, there are some that may have  
>> been used in previous generations and are therefore pseudogenes in  
>> the more traditional sense.
>> cheers
>> Matt
>> On 14 Mar 2006, at 8:53 am, Jane Lomax wrote:
>>> Hi Christine - when you say you assigned GO terms to your  
>>> pseudogenes, do
>>> you mean you assigned the function the pseudogene would have had  
>>> before it
>>> became a pseudogene?
>>>
>>> jane
>>>
>>>
>>> On Tue, 14 Mar 2006, Christiane Hertz-Fowler wrote:
>>>
>>>> Hi,
>>>>
>>>> we have also been struggeling with this for a while during the
>>>> annotation of pathogen genomes. Particularly in the case of the
>>>> Trypanosoma brucei genome which encodes in excess of 1,000  
>>>> pseudogenes
>>>> (out of approx. 9,000 genes). There is experimental evidence that
>>>> fragments/parts of pseudogenes can recombine to produce functional  
>>>> genes
>>>> which are expressed. We have assigned GO terms to these pseudogenes,
>>>> though this is was more for internal purposes at this stage and  
>>>> these
>>>> associations don't make it either into GeneDB or (obviously) the  
>>>> gene
>>>> association files. The definition of a pseudogene as listed below is
>>>> probably in line with this but could possibly be extended to capture
>>>> this oddity. However, I would disagree with not being able to  
>>>> assign GO
>>>> terms to pseudogenes  ...
>>>> contrary to the last couple of e-mails.
>>>>
>>>> Regards,
>>>>
>>>> Christiane
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: owner-annotation at genome.stanford.edu
>>>> [mailto:owner-annotation at genome.stanford.edu] On Behalf Of David  
>>>> Hill
>>>> Sent: 14 March 2006 13:51
>>>> To: Suzanna Lewis
>>>> Cc: Rama Balakrishnan; Sue Rhee; song-devel at lists.sourceforge.net;
>>>> Pascale Gaudet; Barry Smith; GO Annotation list
>>>> Subject: Re: annotating to pseudogenes
>>>>
>>>>
>>>> I agree with Suzi, 100%
>>>>
>>>> David
>>>>
>>>> Suzanna Lewis wrote:
>>>>
>>>>> Hmm, this seems to me to raise some questions regarding dual uses  
>>>>> for
>>>>> unknown. It the case of gene products where you simply do not *yet*
>>>>> known the function they are annotated to 'unknown'. But  
>>>>> conversely, if
>>>>
>>>>
>>>>> we look at the definition from the SO, a pseudogene is clearly
>>>>> something that has *no* function:
>>>>>
>>>>> "Pseudogene: A sequence that closely resembles a known functional
>>>>> gene, at another locus within a genome, that is *non-functional*  
>>>>> as a
>>>>> consequence of (usually several) mutations that prevent either its
>>>>> transcription or translation (or both). In general, pseudogenes  
>>>>> result
>>>>
>>>>
>>>>> from either reverse transcription of a transcript of their "normal"
>>>>> paralog (SO:0000043) (in which case the pseudogene typically lacks
>>>>> introns and includes a poly(A) tail) or from recombination
>>>>> (SO:0000044) (in which case the pseudogene is typically a tandem
>>>>> duplication of its "normal" paralog)."
>>>>>
>>>>> http://song.sourceforge.net/SO_view/index.html
>>>>> (caution, may take some time to load)
>>>>>
>>>>> Annotating pseudogenes to "unknown" implies that they have a  
>>>>> function
>>>>> (but it is not yet known), but pseudogenes have no function by
>>>>> definition, so there is a contradiction.
>>>>>
>>>>> -S
>>>>>
>>>>> On Mar 13, 2006, at 12:02 PM, Rama Balakrishnan wrote:
>>>>>
>>>>>> Hi Sue,
>>>>>>
>>>>>> At SGD, we also annotate pseudogenes to unknown.
>>>>>>
>>>>>> rama
>>>>>>
>>>>>> On Mar 13, 2006, at 11:49 AM, Pascale Gaudet wrote:
>>>>>>
>>>>>>> Hi Sue,
>>>>>>>
>>>>>>> At dictyBase we annotate pseudogenes to unknown.
>>>>>>>
>>>>>>> Pascale
>>>>>>>
>>>>>>>
>>>>>>> At 11:45 AM 3/13/2006 -0800, Sue Rhee wrote:
>>>>>>>
>>>>>>>> Hi all:
>>>>>>>>
>>>>>>>> We are discussing whether/how to annotate to pseudogenes at  
>>>>>>>> TAIR.
>>>>>>>> We are debating whether to annotate them to 'unknown' terms or  
>>>>>>>> not
>>>>>>>> annotate them at all. I'd like to know how the other MODs are
>>>>>>>> handling them.
>>>>>>>>
>>>>>>>> Thanks for your input,
>>>>>>>> Sue
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>> --  
>>>> David P. Hill, Ph.D.
>>>> Senior Scientific Curator
>>>> Mouse Genome Informatics
>>>> Gene Ontology Consortium
>>>> The Jackson Laboratory
>>>> 600 Main Street
>>>> Bar Harbor, ME 04609-1500
>>>> tel:207-288-6430
>>>> htpp://www.informatics.jax.org
>>>> http://www.geneontology.org
>>>>
>>>>
>>>>
>>>
>>> Dr Jane Lomax
>>> GO Editorial Office
>>> EMBL-EBI
>>> Wellcome Trust Genome Campus
>>> Hinxton
>>> Cambridgeshire, UK
>>> CB10 1SD
>>>
>>> p: +44 1223 492516
>>> f: +44 1223 494468
>>>
>>>
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>
>
> -- 
> Pankaj Jaiswal
> G-15, Bradfield Hall
> Dept. of Plant Breeding and Genetics
> Cornell University
> Ithaca, NY-14853, USA
>
> Ph. +1-607-255-3103 / 4199
> fax: +1-607-255-6683
>
>
>
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