Figure 2.
Gene expression profiles. A. Hierarchical clustering on the set of genes (2501) that are significantly (and twofold) different between control and TSC specimens demonstrates a nice separation between the cortical tuber (CT1‐CT4) specimens and autopsy controls (AC). The dendrogram at the top displays the relationship of the samples based on their pattern of gene expression. Each column represents the gene expression profile on one specific array with each row representing the expression level of a specific gene. The expression levels are depicted in three colors; blue: low expression, white: medium expression and red: high expression; deeper shade indicates larger difference. B. Hierarchical clustering on the set of genes (111) that were significantly (and twofold) different between controls and perituberal tissue. The hierarchical clustering on the set of genes that were significantly (and twofold) different shows nice separation between the two groups, indicating that the samples are more similar within each condition. C. Scatter plot showing the correlation between average signal intensities in TSC and autopsy control samples. Data points represent average signal intensity (2log; n = 4 for each condition) calculated from Affymetrix signal intensities for all present genes expressed in the cortical tuber (TSC) and the autopsy control specimens. Red dots represent the significantly changed genes with at least a twofold change in gene expression and a P‐value < 0.01. Blue dots represent the genes that do not fulfill this criterion. D. Scatter diagram of the fold change in the cortical tuber specimens (compared to the autopsy controls) as a function of the P‐value. E. Scatter diagram of the fold change in the perituberal specimens (compared to the autopsy control specimens) as a function of P‐value. The pink dots represent the genes associated with cell adhesion or the immune/inflammatory response.