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[SO-devel] Re: annotating to pseudogenes

Ruth Lovering ruth at galton.ucl.ac.uk
Wed Mar 15 02:12:12 PST 2006


I was just wondering if it would help to use the "NOT"
qualifier.  So that if there is evidence that there may be a
function for the "gene" it would be annotated as "NOT"
pseudogene.  

But perhaps this has already come up.

Ruth

On Tue, 14 Mar 2006 11:29:19 -0700, Karen Eilbeck wrote
> I am late diving in on this because my mail is 
> behaving badly and 64  messages about pseudogenes 
> arrived at once.
> 
> In SO, pseudogenes have no function. If they do, 
> they must be annotated  as the thing they are ie 
> some kind of ncRNA
> 
> There is a relationship between pseudogene and its 
> functional homolog (  a gene) called for the want 
> of a better term  'non_functional_homolog_of'.
> 
> This way you can infer the function the pseudogene 
> would have had if  was a live gene. (Assuming that 
> your genes are annotated with SO and GO  of course!)
> 
> SO is trying to capture what regions of sequence 
> are now as we annotate  them not what they were or 
> will be.
> 
> --Karen
> 
> On Mar 14, 2006, at 10:57 AM, Pankaj Jaiswal wrote:
> 
> > I think the best way to handle this is to effectively
use the  
> > object_type field in the association files. Instead of
using just the  
> > object_type 'gene' by default, try diversifying by using
the types  
> > such as
> > pseudogene/transcript/peptide/mi-RNA/etc.
> >
> > Pankaj
> >
> > 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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> >> _______________________________________________
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> >> https://lists.sourceforge.net/lists/listinfo/song-devel
> >
> >
> > -- 
> > Pankaj Jaiswal
> > G-15, Bradfield Hall
> > Dept. of Plant Breeding and Genetics
> > Cornell University
> > Ithaca, NY-14853, USA
> >
> > Ph. +1-607-255-3103 / 4199
> > fax: +1-607-255-6683
> >
> >
> >
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> > https://lists.sourceforge.net/lists/listinfo/song-devel


******************************************************

Ruth Lovering PhD						
Gene Nomenclature Advisor					

HUGO Gene Nomenclature Committee (HGNC)
The Galton Laboratory
University College London
London NW1 2HE UK
 
URL: http://www.gene.ucl.ac.uk/nomenclature/     
Tel:44-20-7679-5027
Fax:44-20-7387-3496
mailto:nome at galton.ucl.ac.uk 

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