Drug sensitivity analysis in silico

Drug sensitivity data of various tumor cell lines and mRNA expression levels were obtained from the Genomics of Drug Sensitivity in Cancer (GDSC) (www.cancerrxgene.org/) and Cancer Therapeutics Response Portal (CTRP)(https://portals.broadinstitute.org/ctrp/) [34–39]. Pearson’s test was performed to discovery the correlation between gene expression and half-maximal inhibitory concentration (IC50). False discovery rate (FDR)-adjusted p-values were calculated. RNA-sequencing expression (level three) profiles and the parallel clinical records were downloaded from TCGA, and “pRRophetic” R package was applied to calculate the chemotherapy sensitivity of each sample. Based on ridge regression, the IC50 was calculated. All parameters were set as the default values. We removed the batch effect using “ComBat” and set the tissue type to “allSoldTumours” We summarized duplicate gene expression by calculating the mean.