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annotating to pseudogenes
rama at genome.Stanford.EDU
Tue Mar 14 17:16:54 PST 2006
Sue, Suzi, All,
I have been meaning to pipe in earlier but had to deal with a sick
child. any way..
I was going to raise the same question Sue raised in her email about
It is non trivial to determine if a gene is functional or not. We
(SGD) have been debating this issue for a long time now.
This is one of the main reasons why we have left the unknown
So, I would like to know how do other groups decide what is a
pseudogene. Do you use some in house analyses to determine if a
sequence is a pseudogene or do you rely on published literature to
say that a sequence is a pseudogene based on Blah et al?
On Mar 14, 2006, at 4:25 PM, Sue Rhee wrote:
> 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?
> 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
>> 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
>> 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".
>>> As for the SO definition of a pseudogene, I am not sure that I
>>> would say
>>> that all pseudogenes are non-functional.
>>> AgBase Biocurator
>>> Department of Basic Sciences
>>> Box 6100
>>> MS 39762-6100
>>> Mississippi State University
>>> Tel: (+ 1) 662 325 5859
>>> Fax: (+ 1) 662 325 1031
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