[go] total genes/gene products annotated versus genome size

[Karen Christie]

On the subject of pseudogenes, I thought it was agreed some time ago that 
no one should be making GO annotations to pseudogenes because by 
definition they are not producing gene products.

-Karen


On Thu, 20 Dec 2007, Shimoyama, Mary wrote:

> I agree with Judy on this point.  We do not annotate to pseudo genes so
> it is a distortion to include these numbers and as Judy indicated for
> mouse, at this point there would be no figures for functional RNAs in
> rat for which we could possibly have any confidence.  I believe we
> should stick with protein coding genes as the number we use.
>
> Mary Shimoyama
> Program Manager
> Rat Genome Database
> Human and Molecular Genetics Center
> Medical College of Wisconsin
> shimoyama at mcw.edu
> Tel: 414-456-7505
> Fax: 414-456-6595
> http://rgd.mcw.edu
>
> -----Original Message-----
> From: owner-go at genome.stanford.edu [mailto:owner-go at genome.stanford.edu]
> On Behalf Of Valerie Wood
> Sent: Thursday, December 20, 2007 8:28 AM
> To: Judith Blake
> Cc: gene ontology; Sue Rhee
> Subject: Re: Re: [go] total genes/gene products annotated versus genome
> size
>
>
>> Also, I would not favor combining protein coding genes, pseudogenes,
> and
>> functional RNAs in the same set. For one thing, we should not have any
>> annotations to pseudogenes. That was decided some time back. Also, for
>> mouse at least, while we have good algorithms for identifying protein
>> coding genes, we have little or no confidence in any representation of
>> numbers of functional RNAs. So this would lead to a distortion of
>> comparison between genomes.
>>
>>
>
>
> Hi Judy,
>
> I agree that it is best to not to combine these.
> However, using the GO annotation it is not possible to distinguish
> between annotations to protein or non coding RNA (as we only have gene,
> transcript etc) in this column in the association file.
>
> I think we discussed allowing any SO ID, is this ratified?
> and if so does anyone use it?
>
> I think it would be really useful to be able to query GO based on
> 'features that code for proteins' only.
> Otherwise you get artificially inflated categories (for example for
> translation which has all the tRNAs annotated).
>
> I  only manage to make the distinction for pombe and cerevisiae by
> filtering the association files based on the IDs, because I know which
> ID types belong to which features.
>
>
> Val
>
>
>