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annotating to pseudogenes

Alexander Diehl adiehl at informatics.jax.org
Tue Mar 14 07:59:46 PST 2006


My understanding is that when we annotate to genes it is because we 
assume they are the source of a gene-product, which is what we really 
are annotating.  In the case of many pseudogenes there is no mechanism 
available to produce a gene-product, and thus the underlying "gene," 
should simply remain unannotated.

-- Alex


Pascale Gaudet wrote:
> This from the GO guidelines: "There is an important distinction 
> between a gene/gene product annotated to "unknown" function, process, 
> and/or component, and one that has not been annotated. "Unknown" means 
> that someone has tried annotating the gene, but didn't find any 
> information. Absence of annotation implies that no one has looked. "
>
> Also, "unknown" is different from "no function". From the limited 
> information there is on pseudogenes, it seems safer to say that we 
> don't know what they do rather than we know that they don't have a 
> function.
>
> Pascale
>
>
> At 10:38 AM 3/14/2006 -0500, Alexander Diehl wrote:
>> As David and others alluded to earlier, not all pseudogenes are 
>> created equal.  Some may function as the source of anti-sense RNA to 
>> regulate gene function.  Some may serve as the source of material for 
>> gene-conversion processes.  And some may simply be evolutionary 
>> relics not subject to positive selection whatsoever.
>>
>> The first role may be appropriate for GO, as there is a gene-product 
>> involved.  In the other two cases, I think no annotation at all is 
>> appropriate, until and unless an identifiable gene product is found.
>>
>> -- Alex
>>
>>
>> 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
>>>>>>>
>>>>>>
>>>
>>>
>>>
>>
>> -- 
>> Alexander Diehl, Ph.D.
>> Scientific Curator
>> Mouse Genome Informatics
>> The Jackson Laboratory
>> 600 Main Street
>> Bar Harbor, ME  04609
>>
>> email:  adiehl at informatics.jax.org
>> work:  +1 (207) 288-6427
>> fax:  +1 (207) 288-6131
>
>

-- 
Alexander Diehl, Ph.D.
Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
fax:  +1 (207) 288-6131 




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