Additional file 2: Figure S1. of Properties of Boolean dynamics by node classification using feedback loops in a network

Comparison between groups of NFD and non-NFD genes in random networks with respect to the proportions of essential genes, disease genes, and drug targets. In each subfigure, a set of 100 random networks were generated by rewiring the interactions of the signaling networks such that the in-degree and the out-degree of all nodes are conserved. (A) Result of random networks shuffled from KEGG network. The average numbers of NFD and non-NFD genes were 509 and 1150, respectively. The average proportions of essential genes in the NFD and the non-NFD groups were 0.2849 and 0.2852, respectively. The proportions of disease genes in the NFD and the non-NFD groups were 0.2417 and 0.2435, respectively. The proportions of drug-targets in the NFD and the non-NFD groups were 0.2141 and 0.2122, respectively. (B) Result of random networks shuffled from WANG network. The average numbers of NFD and non-NFD genes were 1544 and 4761, respectively. The proportions of essential genes in the NFD and the non-NFD groups were 0.2390 and 0.2413, respectively. The proportions of disease genes in the NFD and the non-NFD groups were 0.2455 and 0.2472, respectively. The proportions of drug-targets in the NFD and the non-NFD groups were 0.1768 and 0.1769, respectively. Figure S2. Changes in the proportion of functionally important genes over the threshold value of the perturbation-sustainable probability in random networks. In each subfigure, a set of 100 random networks were generated by rewiring the interactions of the signaling network such that the in-degree and the out-degree of all nodes are conserved. Given a threshold value β, the y-axis values indicate the average proportions of essential genes, disease genes, and drug targets over the set of candidate genes whose perturbation-sustainable probability is larger than or equal to β in random networks. (A) Results in random networks shuffled from KEGG network. For a reliable comparison, the maximal β was set to 0.0266 which generates 131 candidate genes on average. (B) Results in random networks shuffled from WANG network. The maximal β was set to 0.0908, which results in 121 candidate genes on average. (ZIP 362 kb)