Begin forwarded message:
From: "David H. A. Fitch" <email@example.com>
Date: Fri Oct 24, 2003 9:59:42 AM US/Pacific
To: Eric Haag <firstname.lastname@example.org>, Ronald E Ellis
<email@example.com>, firstname.lastname@example.org, email@example.com,
Subject: gene nomenclature
Gene names are arbitrary (just like taxon names). The main concern is
that they are UNIQUE WITHIN a species (and must therefore be curated).
Because of this, simplicity of nomenclature is key. The
"Spp-gen-123" designation system already works, in the literature as
well as in databases.
It seems most people at least want to use the same gene name for
orthologous genes. But in the (probably many?) cases where there will
be MULTIPLE C. briggsae orthologs for a C. elegans gene and vice
versa, you will need to implement some kind of messy nomenclatural
system. Again, why not simply drop all the complexities, keep it
simple and unique for each species (each of which would bear a
3-letter species designation to maintain its uniqueness as much as
Because of the multiple orthologs "problem", and because orthology
determination must be done a posteriori in the context of gene+species
phylogeny, the best way to show orthology is NOT by gene nomenclature,
but by a correspondence table in the database.
Also, it is REASONABLE that some orthologs have different names.
Orthologous genes in different species may have very different
developmental roles and produce very different phenotypic classes.
Because we have named many C. elegans genes on the basis of phenotypic
class, and because phenotypic classes may be quite different for
different species, why not have different gene names, even for
Dear Ron et al.,
One thing occurred to me on the nomenclature front last night as I
was walking home from work. Why, aside from running out of names,
does it matter whether we mostly use elegans phenotypic classes or
not? Isn't it better to have more accurate names?
The answer, I think, is this: most briggsae genes will have elegans
orthologues. As we start to clone our mutants, if most start off
with briggsae-specific classes we would then have to systematically
change the name of every gene for which that turns out to be the
case. This would plant the seeds of future confusion in the
literature, and that's why I don't like it. The name-changing issue
still exists with my suggestion, the "Cb-unc-A" thing, but at least
the prefix stays the same, and we could make it explicit to all who
care that letters are provisional until the gene is cloned. If it's
novel, the letter sticks; if it's an orthologue it gets switched to
the appropriate elegans number.
This still leaves room for new phenotypic classes where appropriate,
and in some cases genes in these classes will still end up having
named elegans orthologues anyway, but it minimizes confusion. In the
end this differs from Ron's proposal more quantitatively than
qualitatively, I think, but philosophy is important.
Thoughts? Hopefully we're close...
Eric S. Haag, Ph.D. ~
Assistant Professor ~
Department of Biology ~ ~
University of Maryland
College Park, MD 20742 ~ ~ ~
phone: (301) 405-8534 fax: (301) 314-9358 firstname.lastname@example.org
http://www.life.umd.edu/biology/faculty/haag/index.html ~ ~
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