Figure 3

Visualization of expression and correlation in the OXPHOS HG-U133A probes pathway using the pcot2 package. The four red-blue plots represent pairwise correlations between genes in the pathway, with positively correlated genes clustered together. The top left plot relates to the inter-gene correlations observed within the DM2 samples, while the top right plot contains the inter-gene correlation information for the NGT samples, with genes in the same order as the top left plot (i.e., the gene order is the same in both plots on the top row). The same approach is taken in the bottom two plots, with the bottom right plot representing inter-gene correlation within the NGT samples, with genes again grouped by correlation. The gene order in the bottom left plot (DM2 samples) is then the same as that in the bottom right. The gray-scale plots in the center of the figure indicate gene expression intensity, while the red-green plots show the change in expression level (red indicates up-regulation in DM2 relative to NGT).