Fig. 1.

Drug Response Estimation from single-cell Expression Profiles (DREEP). A Construction of Genomic Profiles of Drug Sensitivity (GPDS). The potency profile of each drug in terms of AUC (area under the curve) is correlated with the expression of all messenger RNA across the cell lines for which the drug potency was measured. B Bioinformatics pipeline for the prediction of single-cell drug response. Raw UMI counts are first normalized with the gf-icf pipeline, and then, the most relevant genes in a single cell are used as input for a GSEA against the GPDS ranked list to predict its drug sensitivity. C Performance of DREEP drug sensitivity on 198 cell lines for each set of GPDS signatures used and different numbers of relevant genes to predict the effect of a drug. DREEP’s performance is estimated using either precision-recall curve (upper) or ROC curve (bottom). Max AUC of ROC curves are CTRP2 = 0.691, GDSC = 0.728, and PRISM = 0.661. D Left column: Each point is a drug whose y-coordinate is AUC of the corresponding ROC curve across the 198 cell lines and computed by sorting cell lines from the most to the least sensitive to the drug. Each panel reports the results using different numbers of relevant genes to predict the effect of the drug. Right column: Each point is a cell line whose y-coordinate is the AUC of the corresponding ROC curve obtained by sorting drug predictions from the most to the least sensitive. Each panel reports the results using different numbers of relevant genes to predict the effect of a drug. E Same as C but for the 32 breast cancer cell lines published in Gambardella et al. [5]. Max AUC of ROC curves are CTRP2 = 0.721, GDSC = 0.699, and PRISM = 0.637. F Same as D but for 32 breast cancer cell lines published in Gambardella et al. [5]