IC50 unit of measure

Q&A
1

Hi,

In the file “Drug_sensitivity_AUC_(CTD^2)_subsetted”

Are the IC50 values informed in micromolar? If so, what do negative values mean?

Was the concentratation range (7.8-2000 nM) the same for all the calculated IC50 values?

Thank you very much in advance

2

From the file name, “Drug_sensitivity_AUC_(CTD^2)_subsetted” I’m guessing you generated this file from using the “Custom downloads” tool but also guessing from the name I see that it includes “AUC” so I suspect these values are not IC50s but AUC (area under the curve) values.

If you mean to ask “Was the concentratation range (7.8-2000 nM) the same for all the calculated AUC values?” then, I can answer that: No, I believe the dose range is different per compound.

If I recall correctly, when they performed the CTD^2 drug screens, they choose the dose ranges so that they would capture variation in activity across models. As a result, AUC is very useful for comparing models, but not as useful for comparing compounds.

Thanks,
Phil

3

Thanks, Phil,
I have another question regarding units, but in this case for mutations.
Comparing the following files: “Damaging_Mutations_subsetted” and “Hotspot_Mutations_subsetted” (generated with “Custom Downloads”), I noticed that the later has values of 0 and 1; and the former has values of 0, 1 and 2. I assume that 0 means “no mutations” and 1 means “mutations” for a particular gene and cell line. I was wondering what a value of 2 means and why the Hotspots mutations file doesn’t have any value of 2.

Thank you!

4

You can see file description for the corresponding file in the download section for details: Data | DepMap Portal

But in short I believe the 1 vs 2 refers to whether the mutation was observed with a high-allele fraction or not.

Thanks,

Phil