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Figure 4 | BMC Research Notes

Figure 4

From: Integration of gene expression data with prior knowledge for network analysis and validation

Figure 4

Plot of logarithmic fold-change expression versus pairwise disconnectivity index, colored by membership to a compartment in the bow-tie model of the strictly filtered breast cancer signaling network and box plot of the numbers of differentially expressed tags in the breast cancer case, binned by bow-tie compartment membership. (A) The plot for the strict breast cancer signaling network. Remarkably, most nodes with high disconnectivity have small log fold-change between -1 and 1 (vertical lines). These are ubiquitously expressed genes with high importance for network connectivity. However, there are two exceptions, ERK1 and PDK1, the phosphorylators of RSK. Almost all topologically prominent nodes belong to the largest strongly connected component (LSCC). Moreover, different colors, corresponding to the bow-tie components, show different variability of differential expression. This motivates the next plot. (B) Topologically central nodes are in fact more stably expressed. Logarithmic ratio of number of tags between normal and disease tissue was plotted with the same colors as in (A). Variances differ clearly between groups implying a correspondence between topological features and expression: Central molecules, i.e. those of the LSCC, have strong tendency to be not differentially expressed, showing that these are molecules which are essential to the cell's functioning.

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