Hi,
I have been looking into pleural mesothelioma and screening for synthetically lethal targets in NF2-mutant cases. Only two cells lines have been identified as NF2-mutant PM, however a third cell line also contains damaging mutations. I was wondering why this is, and why it is has been categorised as an NF2-WT PM cell line, the cell line of interest is NCIH2052. I have attached my graph. Many thanks.
Hi,
Thanks for reaching out. Could you clarify where the “NF2 mutant/NF2 WT” annotation is from, so we can reproduce the plot? Happy to look further into this discrepancy.
Simone
Thanks for sharing the details. I was able to reproduce it and it seems to be a bug where the mutation annotation in context manager is performing filtering strangely. While we look into this, I’d recommend creating contexts using mutation as a “matrix dataset” instead of annotation. This ensures that information is directly pulled from the dataset itself. See below:
Thanks for bringing this to our attention!
Simone
Great Thankyou. Another Question. For shiny depmap v 2.0 I understand you use data from depmap 19Q3 in the gene essentiality tool. I am unable to locate the number of cell lines used from shRNA within this. I have located the 625 cell lines used in CRISPR screens, but not RNAi. Many Thanks, Emilia
shinyDepMap is not created or maintained by us, so you might want to direct this question to the developers. The RNAi data on our portal can be found under Data | DepMap Portal > DEMETER2 Data v6.
Simone
