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annotating to pseudogenes

Suzanna Lewis suzi at fruitfly.org
Tue Mar 14 08:28:30 PST 2006


We went through all of this before and basically, the ultimate word 
from the biologists, was that pseudogene means "it is broken, and has 
*no* function". In other words, things that have any sort of 
functionality—whether by recombination, anti-sense, et cetera—are 
*not*, by definition pseudogenes. They are then gene products of a 
class that do have a function, and there a plenty of terms to describe 
these classes in SO (cassetes, ncRNA, and so on).

While I realize that many communities are sloppy (errr, fuzzy, 
ambiguous, whatever), we are trying to use careful definitions in the 
GO and SO community. This is essential if we are ever to be able to 
compute on these data. Therefore, within the GO community, if you say 
something is a pseudogene, you are saying explicitly that it has *no* 
function. If it may have a function, then it is *not* at pseudogene. 
I'm beginning to repeat myself, that's all for now.

-S

On Mar 14, 2006, at 7:59 AM, Alexander Diehl wrote:

> 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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