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[SO-devel] Re: annotating to pseudogenes

Pankaj Jaiswal pj37 at cornell.edu
Tue Mar 14 07:08:00 PST 2006


Here is one more
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16229821&query_hl=1&itool=pubmed_DocSum
Oct4 pseudogenes are transcribed in cancers. Results suggest that 
pseudogenes Oct4-pg5 and Oct4-pg1 may be involved in the regulation of 
Oct4 gene activity thus might be pertinent to carcinogenesis. 
Transcription of these Oct4 pseudogenes may have contributed artifacts 
to the current knowledge of Oct4 gene expression and function in cancers.

Pankaj

val at sanger.ac.uk wrote:

> But there is alway one....
> 
> PMID: 12721631
> 
> Nature. 2003 May 1;423(6935):91-6.	
>  
> An expressed pseudogene regulates the messenger-RNA stability of its homologous 
> coding gene.
> Hirotsune S, Yoshida N, Chen A, Garrett L, Sugiyama F, Takahashi S, Yagami K, 
> Wynshaw-Boris A, Yoshiki A
> 
> 
> 
> 
> 
> Quoting chris mungall <cjm at fruitfly.org>:
> 
> 
>>Yes, I agree. pseudogenes have no function by definition, so they would  
>>have no GO annotation.
>>
>>On Mar 13, 2006, at 3:48 PM, 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
>>>>>
>>>
>>>
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> 
> 
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-- 
Pankaj Jaiswal
G-15, Bradfield Hall
Dept. of Plant Breeding and Genetics
Cornell University
Ithaca, NY-14853, USA

Ph. +1-607-255-3103 / 4199
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