Fig. 3

Changes in gene expression in the Htt-Q23 control versus Htt-Q74 HD cell line. a First two principal components of the pre-processed microarray data corrected for potential slide effects using ComBat. Each symbol corresponds to a single microarray. The different time points are shown in colour. Dots represent the data obtained from the Htt-Q23 control cell line and triangles the data from the Htt-Q74 HD cell line. The first principal component (PC1) separates control from HD microarrays whereas the combination of PC1 and PC2 separates early (0-36 h, indicated in the red oval) from later (48-120 h, indicated in the blue oval) time points in the Htt-Q74 HD cells. Three of the 24 h samples from the HD cell line did not group with the other early samples, however. This separation between early and late samples was not observed in the Htt-Q23 control cells. The numbers on the axes indicate the percentage of variance explained by the plotted principal components. b Changes in the number of significantly DE genes were examined over time. Expression values of all genes at each time point were compared to pre-induction state (time = 0 h). Positive numbers on the y-axis indicate the number of genes found to be up-regulated whereas negative numbers indicate the number of down-regulated genes (adjusted P-value < 0.05). The change in the number of DE genes over time is plotted separately for the control (blue) and HD (red) samples and finally for the HD samples after correction for the response detected in the control samples (orange)