X and Y axis meanings

Q&A
1

Dear DepMap members, I am interested in checking the drug sensitivity of melanoma lines to atorvastatin drug in relation to the LDLR protein levels. I created a graph but not sure what X and Y mean exactly. I am attaching a screen shot of the graph.
Specific questions are

  1. Do positive values on Y axis indicate the drug is more toxic to cancer cells? What is the definition of Drug sensitivity and what assay was used to determine it?
  2. On X axis, what is the meaning of numbers from -2 to +1? Is this expression level arbitrary when cells were treated with this compound and vehicle control followed by mass spec? -2 means 2 fold reduction in the expression levels of LDLR?
    LDLR
    LDLR1803×886 103 KB

Thanks,
VJ

2

Hi VJ,

  1. In this case the y-axis represents cell viability (log2 fold change of estimated cell abundance of drug-treated cells compared to controls). This is using the PRISM assay. You can refer to this paper for more details.

  2. The x-axis data in this case are taken from the proteomics data described in Nusinow et al, and represent relative protein abundance. For the precise interpretation of these values, please see this guide.

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3

Hi James, thank you very much for the reply. I am still confused with this, please let me know if I am correct:
A value on Y axis higher than 0 means cells are growing and hence less sensitive to be killed by a drug? Like in this graph higher expression of LDLR (let’s say LDLR, X axis value is 1.5 and Y axis value is -3) is making cells susceptible to be killed by atorvastatin?
Best,
VJ

4

Hi VJ,

Larger magnitude values on the y-axis mean less sensitivity to the drug, yes. 0 represents no log-fold change viability measured relative to vehicle control.

This plot indicates that cell lines with higher LDLR protein levels tend to be more sensitive to the drug

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