Figure 4

Classification of lost edges. The figure illustrates four examples of loss of correlation in tumor network edges. For each subfigure (4A-4D) the upper left plot shows the paired expression values of the TF (left) and the target gene (right) across normal samples. Similarly, the upper right plot contains the expression values across tumor samples. Lower plots show the correlation between the TF (x-axis) and the target gene (y-axis) expression for the normal samples (left) and the tumor samples (right). Blue dots correspond to expression values in normal adjacent mucosa samples and red dots correspond to expression values in tumor samples. A) Loss of transcriptional interaction mediated by silencing of both the TF and the target gene simultaneously. This category comprises 0.2% of lost edges (n = 80). B) Loss of transcriptional interaction mediated by silencing of the target gene only. This category comprises 2.1% of lost edges (n = 1,105). C) Loss of transcriptional interaction mediated by silencing of the TF only. This category comprises 1.7% of lost edges (n = 923). D) Loss of transcriptional interaction with no TF or the target gene silencing. About 96% of lost edges in the tumor network (n = 50,882) fall into this last category.