[Bioperl-l] GeneStructure & Promoter(s)
Samuel Aparicio
saparici@hgmp.mrc.ac.uk
Mon, 19 Feb 2001 09:47:40 +0000
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Ewan Birney wrote:
This is not such a bad idea. I guess regulatory_elements in my view would
> be on the gene (not the Transcript). But this is serious "no one really
> knows what is going on" terroritory. It would not kill me if we did not do
> this at all...
>
> > I've got some time on Monday (tomorrow for me, today for Europe).
> > So, please give feedback, I'd really enjoy the GeneStructure
> > modules being useful and reasonably stable at the same time.
> >
I agree, in part. It certainly makes better sense to attach regulatory
elements to the gene, but
I would gently make two points here. The first is that many biologists will
consider
a promoter to be a regulatory element: so from this point of view I would say
there might be a good
case for considering RegulatoryElement as the superset and promoter,
enhancer
or whatever else as the subsets. The second point is that it may be worth at
least considering the issue of having definitions in place, even if other
pressures
prevent an implemented set of applications, because one of the key interests
of comparing vertebrate genomes will be identification of putative regulatory
elements
within the human genome, of all class types. This will become an issue very
soon. :-)
Sam
--
Dr Samuel Aparicio BMBCh PhD | saparici@hgmp.mrc.ac.uk
Principal Investigator, University Dept. Oncology,
Wellcome Trust Centre for Molecular Mechanisms in Disease
Cambridge CB2 2XY. UK. | +44 1223 762663 (tel)
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Ewan Birney wrote:
<p>This is not such a bad idea. I guess regulatory_elements in my view
would
<blockquote TYPE=CITE>be on the gene (not the Transcript). But this is
serious "no one really
<br>knows what is going on" terroritory. It would not kill me if we did
not do
<br>this at all...
<p>> I've got some time on Monday (tomorrow for me, today for Europe).
<br>> So, please give feedback, I'd really enjoy the GeneStructure
<br>> modules being useful and reasonably stable at the same time.
<br>></blockquote>
I agree, in part. It certainly makes better sense to attach regulatory
elements to the gene, but
<br>I would gently make two points here. The first is that many biologists
will consider
<br>a promoter to be a regulatory element: so from this point of view I would
say there might be a good
<br>case for considering RegulatoryElement as the superset and promoter,
enhancer
<br>or whatever else as the subsets. The second point is that it may be
worth at
<br>least considering the issue of having definitions in place, even if
other pressures
<br>prevent an implemented set of applications, because one of the key
interests
<br>of comparing vertebrate genomes will be identification of putative
regulatory elements
<br>within the human genome, of all class types. This will become an issue
very soon. :-)
<br>Sam
<br>
<pre>--
Dr Samuel Aparicio BMBCh PhD | saparici@hgmp.mrc.ac.uk
Principal Investigator, University Dept. Oncology,
Wellcome Trust Centre for Molecular Mechanisms in Disease
Cambridge CB2 2XY. UK. | +44 1223 762663 (tel)</pre>
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