From: Ronald E Ellis <ron.ellis@umdnj.edu>
Date: Fri Oct 24, 2003 11:54:58 AM US/Pacific
To: Eric Haag <ehaag@wam.umd.edu>
Cc: pws@caltech.edu, dave.pilgrim@ualberta.ca, david.fitch@nyu.edu
Subject: Re: nomenclature non-elegans genetic

Dear Eric, Paul, Dave and David,

I realize there might be frequent name changing, because some C. briggsae names will be swapped for ones based on clear orthologs from C. elegans.

However, I would find it easier to keep track of these changes if they didn't involve the same three-letter gene name.  For me, going from Cb-unc-F to Cb-unc-36, or unc-cb-6 to Cb-unc-36, or even worse, from Cb-unc-6 to Cb-unc-36 would be confusing.  I would like a C. briggsae name that could be kept and used for its own sake, even if a second one, based on molecular comparisons with C. elegans, were also to be adopted.  In fact, I have to agree with David that one could make a strong case for not changing gene names even if there are clear orthologs.

In either case, what I most want to avoid is a situation like that involving S. cerevisiae and S. pombe cell cycle mutants, where the same gene has two similar names, but with different numbers.  Lots of people find that confusing.

Ron



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

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                                          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        ehaag@wam.umd.edu
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                                    "I'd rather be here now."

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Ronald Ellis
Associate Professor of Molecular Biology
The UMDNJ School of Osteopathic Medicine
316-317 Science Center
Two Medical Center Drive
Stratford, NJ 08084

Phone:    (856) 566-2768
FAX:     (856) 566-6291