Simulating the effect of experimental perturbation on a real biological signaling network in SiGNet.

<p>SiGNet was used to simulate the effect of EGF treatment on EGFR and its downstream proteins, and the simulated data tested against published experimental data [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177701#pone.0177701.ref032" target="_blank">32</a>]. (<b>A</b>) Schematic showing the network structure, which was based on interactions reported by Blagoev et al. The network was drawn in Cytoscape and used as an input for SiGNet. (<b>B</b>) Data simulated for the network in (A) using SiGNet, with and without the optional decay function. Data shown are mean values calculated from ten ‘experimental replicates’. Pearson correlations between simulated and real data are shown. Additional simulations of this network incorporating simple feedback mechanisms are illustrated in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177701#pone.0177701.s002" target="_blank">S2</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177701#pone.0177701.s003" target="_blank">S3</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0177701#pone.0177701.s004" target="_blank">S4</a> Figs.