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annotating to pseudogenes

Sue Rhee rhee at acoma.Stanford.EDU
Tue Mar 14 16:25:55 PST 2006


Suzi and all,

Is SO defining sequence elements based not only on the structural/genome 
context, but also on functional attributes? If so, I think the 
definition of SO's pseudogene is perfectly reasonable. Otherwise, I 
question whether the 'non-functionality' part of the definition for a 
pseudogene is appropriate in SO.

Even if we stick to SO's definition of a pseudogene, it is not trivial 
to unequivocally determine that a sequence element is non-functional 
(unless there are explicit, agreed upon criteria for determining 
non-functionality that I am not aware of).

It appears that we have two choices here: One is to be more restrictive 
about calling something a 'pseudogene' in our databases based on a set 
of agreed upon criteria (e.g. expression, assigned role/function, 
anything else?). Two is to define a pseudogene without the functionality 
component and annotate them to unknown unless there is a function/role 
defined.

These are difficult choices to make, with pros and cons for each. I'm 
happy with sticking to either choice if we could reach a group 
consensus. Do you all think this would be possible? How can we best do this?

Thanks,
Sue


Suzanna Lewis wrote:
> 
> On Mar 14, 2006, at 8:35 AM, Fiona McCarthy wrote:
> 
>> Hi All,
>>
>> I recent found a microarray tiling paper (PMID: 15876366) where the
>> authors estimated that one fifth of human pseudogenes on chr22 are
>> potentially transcribed. It seems to me that there must be a reason for
>> this level of transcription, even if we don't know what it is.
>>
>> I think it would be reasonable to annotate pseudogenes to GO, even if we
>> have to use function unknown in most cases. Otherwise, we would be
>> implying that *all* pseudogenes have no function, and this may not be the
>> case.
> 
> See Peter's reply.
> 
> But to repeat.
> 
> All pseudogenes are, by our definition, things that you believe are 
> truly and sincerely, completely, uttterly dead (shades of the dead 
> parrot skit).
> 
> If, in your scientific judgment, they may have some function (including 
> latent, waiting for recombination, function a la inactive, cold-storage 
> units) then they are not pseudogenes: in our shared, common definition.
> 
> We have agreed that it is useful to have clear definitions, and that we 
> will use the same terms to mean precisely the same thing. We must not 
> fall away from this.
> 
> While we are aware that there are entire communities that use the term 
> "pseudogene", but mean something different, we must be consistent 
> ourselves. Which means that we must have other terms (with the synonym 
> "pseudogene") to describe these different phenomena.
> 
> Now, part 2.
> 
> Given that this thing has a function, then you get into the issue of 
> what is that function. Once you have agreed that the function is in 
> there, it is perfectly fine to say "unknown".
> 
> -S
> 
>>
>> As for the SO definition of a pseudogene, I am not sure that I would say
>> that all pseudogenes are non-functional.
>>
>> Fiona
>>
>>
>> AgBase Biocurator
>> Department of Basic Sciences
>> Box 6100
>> MS 39762-6100
>> Mississippi State University
>> USA
>> Tel:   (+ 1) 662 325 5859
>> Fax:  (+ 1) 662 325 1031
>>
>> http://www.agbase.msstate.edu/
>>



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