Dear DepMap forum,
Hi, I have questions about the PRISM 19Q4 dataset.
While I checked the secondary-screen-replicate-treatment-info.csv file, some drugs are not targeting the genes. (i.e., NA value in target column)
It would be a problem when I construct the adjacency matrix between drugs and targets for network-based analysis.
Because when the targets are NA, this pair will be set to 0 in the matrix.
Can anyone suggest how to preserve those cases in the drug-pair matrix?
Also, is there any plan for updating the PRISM dataset?
If anyone knows the further plan about the PRISM, please announce to me.
The updates for PRISM Repurposing dataset are not regular, we are expecting an update to the Primary dataset (@2.5 uM) in the following months but there is no planned updated for Secondary dataset yet.
For the annotated targets, unfortunately for most compounds we don’t have the relevant annotations (or have vague annotations). As DepMap portal, we are following the annotations published and maintained at repurposing-app on REPURPOSING .
Unfortunately, I don’t have good suggestion for filling in NA’s in a target/drug matrix. You may try to fill in some of the targets by parsing MOA annotations, but for most of the drugs I would drop them from such an analysis.
Hope this helps.
Dear Mr. Mustafa,
Thank you for your kind and detail reply!
I fully understand the NA target now, and I temporarily excluded them for following analysis.
I’ll keep in mind your suggestion.