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. 2010 Aug 19;6(8):e1000889. doi: 10.1371/journal.pcbi.1000889

Figure 3. Comparison of coherence of node values in highest scoring networks.

Figure 3

A) Boxplots of gene expression change values (1 µM DOX, 24 hours relative to control) of nodes in networks generated by different cutoffs of EF values, or in networks generated by Ingenuity Pathway Analysis software using different gene expression value cutoffs for the focus gene set (see Methods). B) Heatmaps showing position of genes in the networks in A in the whole data distribution. Positions of genes in the respective networks are indicated by a white line. C) A network of nodes generated by Ingenuity Pathway Analysis software with focus gene set using 1.5 as cutoff. Since original network plots in IPA lack node colorings for intermediate genes (non-focus genes), we extracted all nodes in the IPA-generated network and re-plotted them using our network, where we colored all nodes by their gene expression change.