If I remember correctly, back in the ACeDB days it was possible to find positive/negative data for balancers, i.e. genes that were known to be balanced by a certain balancer and, just as importantly, genes that were known not to be balanced. This was very helpful. I cannot for the life of me figure out how to find that information. I know that Mark Edgley’s WormBook chapter on balancers gives information like “balances LG I from the left end to unc-13,” but sometimes I want to know the next gene tested that it does NOT balance. Also, is there a way to provide wormbase info if you’ve tried to balance a gene with a balancer and found that it worked or did not work?
I use the table from the old CGC genetic maps (for example, page 73 of the 2003 Genetic Map), but that’s the same information in Edgley’s chapter, albeit I find it more convenient.
I haven’t easily found what you’re looking for. You can always go digging in the AceDB in the Tree display within WormBase (and it looks like you should do this in the old legacy WormBase site, as I can’t seem to pull up mapping data in WormBase 2.0). It wasn’t obvious to me how to find this particular information within the ACeDB data, though. If for example I look at the mapping data for unc-59, in the convenient Mapping Data tab instead of the less convenient Tree Display, I don’t see any mapping experiments involving hT2, even though unc-59 defines one of its endpoints and so some mapping experiments must have happened.
Keep in mind: so far as I know, very few of the molecular breakpoints of the balancer chromosomes have been determined. nT1 aka n300 has, because finding its breakpoint could solve a question about vulval development - but offhand I don’t know if any others have. So all we’d have most often is mapping experiments involving convenient visible phenotypic markers. Yeah, the balanced region probably extends a bit beyond the last visible marker and doesn’t reach the next convenient one, and it could be more closely defined - but it probably hasn’t been, and likely won’t.
If you’re interested in a small number of genes, you can use the legacy site’s Rearrangement page, located at http://legacy.wormbase.org/db/gene/rearrange?. Use the syntax ‘includes:GeneName’ or ‘excludes:GeneName’ to obtain lists of the relevant rearrangements.
For more systematic queries, you’ll probably need to download the data (or use the WormMine API) and create a script to extract the information you want.
@ Sperm or Egg
I tried that yesterday. It works beautifully for Dfs and Dps, but I couldn’t find such data for balancer chromosomes (ie a couple of reciprocal translocations I looked at). Are you able to find such?
To look at individual Dfs and Dps you don’t need the legacy site and can use the current WormBase 2.0 . If you want to access individual mapping experiments you will need to use the legacy site (because of the bug I noted yesterday, which has been reported).
For finding Dfs and Dps I’d strongly recommend the old CGC genetic maps as a starting point; see the link in my earlier comment. I don’t know whether you can do the search you describe on the current WormBase 2.0 site.
Hi Hillel,
It appears that the legacy site includes balancers, but the search by gene function only returns those that have been validated while excluding those that can be inferred from the endpoints. For example, includes:unc-4 returns mC7 and mT1.
It also appears that the data are incomplete for the legacy site. A test for unc-101 does not return hT2, and dpy-17 returns mT1 but not hT2.
Conversely, searching dpy-17 under Rearrangements on the current site returns hT2 but not mT1. But the mT1 rearrangement page lists dpy-17 as a positive marker, so it’s unclear how the data are represented for searching.
We should probably let the WormBase team know. Do you want to do it (you uncovered the bug), or shall I?
-Harold
Harold,
This is all very confusing. I think you should make the new bug report, you’ve got a better handle on this issue.
Hillel,
I’ve reported the bug to WormBase. I’ll let you know what they have to say.
From the WormBase development team:
“Thanks for the bug report on rearrangement search. It was indeed caused by a failure of the search functionality. It’s fixed now on our testing site: http://staging.wormbase.org/search/rearrangement/dpy-17 You can find other rearrangements related to dpy-17. But please be reminded that the testing site is an unstable development version of WormBase website. This bug fix will be live later this month.”