Number of screened compounds

Q&A
1

For how many compounds does DepMap include publicly available sensitivity data and for how many cell lines?

2

The next update of the portal will include these numbers on the data overview figure, but in the mean time, I’ll post the number of compounds per dataset here taken from the dev version of this figure:

The CTD^2 dataset on the portal includes 545 compounds.
The PRISM Drug Repurposing screen on the portal includes 6765 compounds.
The GDSC dataset on the portal includes 175 compounds.

Thanks,
Phil

3

Dear Phil,

thank for replying. For the PRISM data set, have all these 6765 compound been screened in more than 900 cell lines?

I am writing a review and would like to mention these data. Therefore, I have to give these numbers.

Kind regards,

Slava

4

No, that’s a good point, the PRISM dataset is actually assembled from multiple screens, and the earlier screens were performed on fewer cell lines then the later screens. As a result, some compounds were screened against more cell lines than others.

If one wants the most accurate answer, really the best thing to do would be to download Repurposing_Public_24Q2_Extended_Primary_Data_Matrix.csv and count the non NA values per compound. (This will also take into account that some cell lines in some compounds failed QC)

That file contains all the primary screening data from the original screens which were published in Discovering the anticancer potential of non-oncology drugs by systematic viability profiling | Nature Cancer along with additional screens which were generated and released after the paper was published.

Thanks,
Phil