Subject: Re: existence-uncertain genes
...
>
> > Dear Sima,
> >
> > thanks for the reply.
> > I'll compile a list of the existence-uncertain CGs that I find as genes
> > that change in various array experiments. I am also in the process
> > of doing a relatively large number of in situ's on these genes; do you
> > want to wait until I have that data , or would you want me to send the
> > information as I have it right now ?
> >
> > In any case, I just found the following three uncertain genes to show
> > reduced transcript levels in ribbon (rib) mutant embryos compared to WT
> > embryos. If I look more carefully through all my experiments, there will
> > certainly be more. I'll keep in touch and let you know when I have all the
> > info together.
> >
> > CG13064
> > CG10394
> > CG17588
> >
> > cheers
> > Stefan
> >
> > >Dear Stefan,
> > >
> > >Thank you very much for your message. We did detail our methods in
> > >re-annotating the genome to create Release 3.1, both in this paper
> > >
> > >http://genomebiology.com/2002/3/12/research/0083
> > >
> > >and at
> > >
> > >http://www.fruitfly.org/annot/reannot-guidelines.html
> > >
> > >Basically, if a gene encoded a small protein (<50aa) we required there to
> > >be experimental evidence in FlyBase for its existence. However, since
> > >these checks were done by hand, sometimes a curator missed a piece of
> > >experimental evidence, and a gene was mistakenly deleted. It sounds as
> > >though CG13064 is a case of such a gene that should be reinstated in a
> > >future release.
> > >
> > > > I'd be happy to compile a list of the existence-uncertain genes
> that I've
> > > > come across in my array experiments.
> > >
> > >That would be wonderful. If you sent such data to
> > >flybase-updates, we could curate it as a personal
> > >communication from you, and then we could reinstate the genes based on
> > >attributable evidence.
> > >
> > >Thanks very much,
> > >
> > >Sima Misra
> > >FlyBase BDGP
> > >
> > > > ___________________________________________________________
> > > > Stefan Luschnig, Ph.D.
> > > > Department of Biochemistry/HHMI
> > > > 279 Campus Drive, Beckman Center Rm. B453
> > > > Stanford University School of Medicine
> > > > Stanford, CA 94305
> > > > USA
> > > > ____________________________________________________________
> > > >
> >