List of missing RNAi clones?

Model Organism: Worms Scientific Discussion
1

Hi folks,

Is there a (fairly comprehensive) list somewhere of the genes NOT represented in the major RNAi bacteria / clone libraries?

Thanks,
Curtis Loer

2

Hi Curtis,

there are like 1470 coding C.elegans genes still without RNAi data (which I guess is a rough analog to not in a RNAi library) in WS252.
I do believe it will be soon possible to query it in WormMine, but for this release I attached the list to the post.

M

[EDIT: I haven’t removed the mitochondrial genes from the list]

3

Hello

More than a third of the genes (512) in Michael’s list are in fact targeted by one or more clone, most often by clones in the Ahringer top-up collection (sjj2_ clones).

I generated the attached using our published Clone Mapping tool

http://bioinformatics.lif.univ-mrs.fr/RNAiMap/index.html

Go to the tab “Find targets”, enter the list of WBid names, select WBids as “Input Type”, and “target score” >=100 for high confidence hits.

Hope that helps

PS. The tool is also good for checking whether a sequenced clone is what it is supposed to be (“Map your clone” tab).

4

thanks Jonathan :slight_smile:

… and as a shameless plug: if anybody phenotypes the clones, please submit the observed (and also the looked for, but not observed) phenotypes to us :wink:

5

Thanks to mh6 and Jonathan – I also noticed that plenty genes in the mh6 list were found in Ahringer libraries. So, just to clarify, I should be able to have a closer-to-correct list of
unrepresented genes by deleting from mh6’s list those found by JE via the Clone Mapping tool.

I suppose some of those lacking RNAi info might also be clones that don’t grow from one or more of the libraries, but may appear represented…

Curtis