Result of cell line investigation, signature selection, and quality control. A) The clustergram of expression samples from (HDAC) families of enzymes. Hierarchical clustering of 175 expression samples treated by drug TRS A. Rows and columns represent genes and samples, respectively. Columns were labeled with cell line (top) or concentrations (down). Clusters can be clearly observed and further examination of samples in the same cluster reveal that they are all from the same cell line. However, no such correspondence presented for the drug concentrations. This suggested that drug effectiveness is cell line dependent. B) Example of Quality Control. The heatmap and pair-wise two-sample scatter-plot of 4 cMap samples from the same drug were shown. They revealed that only two samples showed similarly and the other two did not. In this example, sample s2 and s4 were removed as noise. C) Example of Signature Gene Set Selection. Two-sample scatter-plots of the selected gene signatures for three drugs were plotted. The red cross dots represented the selected genes and the black dots represented the rest of gene. Tables contain the symbols and expression up- or down- regulation for the selected genes of the three drugs.