Fig. 4

Cellular transcriptomics results. (a) Venn diagram of differentially expressed genes identified by RNA-Seq in the different vandetanib doses compared to DMSO. (b) Two-dimensional reduction of the 500 genes with the highest variance in the variance-stabilized RNA-Seq dataset by principal component analysis (PCA). Black squares, yellow dots, orange triangles and red diamonds indicate the DMSO control, EC10, EC50 and EC80 dose, respectively. Ellipses represent 95% confidence intervals (CIs). (c) Three-dimensional reduction of the variance-stabilized RNA-Seq data by sparse partial least-squares discriminant analysis (sPLS-DA). Tuning of the model resulted in choosing three components with 50, 40 and 25 factors each. The plots show the samples in the first and second (left) and in the second and third (right) dimensions. Black squares, yellow dots, orange triangles and red diamonds indicate the DMSO control, EC10, EC50 and EC80 dose, respectively. Ellipses represent 95% CIs. (d) Heatmap representing the variance-stabilized (vst) expression data of the 94 genes identified as differentially expressed in all three vandetanib treatments compared to DMSO. (e) Heatmap representing the variance-stabilized (vst) expression data of the 52 genes that were picked by the sPLS-DA model and significantly differentially expressed in at least one vandetanib dose compared to the DMSO control.