Subject: Fwd: gene nomenclature
From: Paul Sternberg
Date: Fri, 24 Oct 2003 16:33:36 -0700
CC: Paul Sternberg

Begin forwarded message:

From: "David H. A. Fitch" <>
Date: Fri Oct 24, 2003  9:59:42 AM US/Pacific
To: Eric Haag <>, Ronald E Ellis <>,,,,
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 possible).

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 orthologs?


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...



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Paul W. Sternberg
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