Hello,
In previous/earlier updates of DepMap, the Avana screens contained MARCH5 (now MARCHF5). The latest version that contains it was likely 20Q4. However, I checked again recently (21Q2/3) and it’s now gone from the CRISPR screens.
Can you look into what could have happened during the updates? I’m a bit worried that the removal of MARCHF5 in the database now puts into question the co-dependencies I downloaded for MARCHF5 last year.
Thanks!
I just did a quick search and I could find this gene on the portal, Chronos and CERES 21Q3, you can also try the download option on the right corner of plots. are you looking at a specific cell line?
https://depmap.org/portal/gene/MARCHF5?tab=dependency&dependency=Chronos_Achilles
Thanks Vida. This is interesting — but the MARCHF5 CRISPR co-dependencies do not seem to show up in the main page (it only shows RNAi). It also disappears altogether as the top co-dependency from the MCL1 list (it was there in 20Q4). I also could not find MARCHF5 in the full top 100 co-dependency file for 21Q3 (the rest of the genes remain). Is this a glitch or did the score really drastically changed?
Thanks for letting us know. The relationship with MCL1 remains strong. We’ll look into what happened with MARCHF5’s page on the portal.
Thanks Joshua. It may have something to do with the renaming of these genes (or their original names are reformatted as dates in Excel). I noticed that the CRISPR co-dependencies of the other MARCHF genes (formerly “MARCH” genes), SEPT genes and DEC genes do not show up on the main portal.
A fix for this has been deployed. The underlying issue is that MARCHF5 is not present in the Project Score dataset, and as a result is not included in the combined CRISPR dataset that we show by default.
To avoid this problem in these cases, we fall back to the Achilles CRISPR dataset which does have the gene present. (The top of the tile always says which dataset the distribution was taken from.)
