Geometric Interpretation of Gene Coexpression Network Analysis
Figure 4
Module eigengenes in the brain cancer gene coexpression network.
(A) The pairwise scatter plots among the module eigengenes E(q) of different modules and cancer survival time T. Each dot represents a microarray sample. ME.blue denotes the module eigengene E(blue) of the blue module. Numbers below the diagonal are the absolute values of the corresponding correlations. Note that the module eigengenes of different modules can be highly correlated. The brown module eigengene has the highest absolute correlation (r = 0.20) with survival time. Frequency plots (histograms) of the variables are plotted along the diagonal. (B) Upper panel: heat map plot of the brown module gene expression profiles (rows) across the microarray samples (columns). Red corresponds to high- and green to low- expression values. Since the genes of a module are highly correlated, one observes vertical bands. (B) Lower panel: the values of the components of the module eigengene (y-axis) versus microarray sample number (x-axis). Note that vertical bands of red (green) in the upper panel correspond to high (low) values of the eigengene in the lower panel. (C) The expression profile of the module eigengene (y-axis) is highly correlated with that of the most highly connected hub gene (x-axis). A linear regression line has been added.