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annotating to pseudogenes

Matthew Berriman mb4 at sanger.ac.uk
Tue Mar 14 13:49:26 PST 2006


..in which case, we may need a new SO term to describe them ;-)

Matt




On 14 Mar 2006, at 2:45 pm, Suzanna Lewis wrote:

> Right, it is in the traditional sense that we are using the term 
> "pseudogene" (our 1 single definition). The others erstwhile 
> "pseudogenes" are horses of a different color entirely and we must not 
> confuse the two.
>
> -S
>
> On Mar 14, 2006, at 9:02 AM, 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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