Worm identifiers

John Murray's Avatar

John Murray

25 May, 2013 03:57 PM

I have long found treefam an indispensible tool for looking at orthology relationships between my model organism of study (C. elegans) and other species. While, I appreciate what TreeFam is trying to do in standardizing gene nomenclature on the trees, the new version is much harder to use for this purpose. The problem is in the choice of "systematic" name as the only display option. For example the C. elegans t-box TF gene tbx-37 also has the (non-human-readable) name Y47D3A.12.2. In older versions the treefam displays showed the various C. elegans t-box names (tbx-8, tbx-9, tbx-2, etc) in their appropriate place in the tree. In my opinion this should be the default, or at least an option. It appears the only way to get this information currently is to click through gene-by-gene to ensembl?

  1. 1 Posted by Fabian on 03 Jun, 2013 12:41 PM

    Fabian's Avatar

    Hi John,
    thanks for your suggestion.
    Just to give you an update. We have looked into that and are working on a solution behind the scenes.
    Since most of our source IDs are from Ensembl or Wormbase, a solution will be along the lines of providing a mapping between Ensembl/Wormbase ID to its associated gene name (e.g. tbx-37).
    That should make the trees a lot more readable. Once we have that in place, we let you know.

    Thanks again for the useful suggestion!

    Cheers,
    Fabian

  2. Matthieu Muffato closed this discussion on 16 Jun, 2020 04:09 PM.

Comments are currently closed for this discussion. You can start a new one.

Keyboard shortcuts

Generic

? Show this help
ESC Blurs the current field

Comment Form

r Focus the comment reply box
^ + ↩ Submit the comment

You can use Command ⌘ instead of Control ^ on Mac