Additional file 1: Figure S1. of Construction and analysis of gene-gene dynamics influence networks based on a Boolean model

Pseudo-code for the Barabási-Albert model. It describes the algorithm to construct random network in Barabási-Albert model which is a type of network growth model. Figure S2. Pseudo-code for the shuffling model. It describes how to construct random network using shuffling model which rewires the edges of GMI network in a way that in-degree and out-degree of all nodes are preserved. Figure S3. Visualization of the GMI and the corresponding GDI networks in the case of ABAN. (a) The GMI network with ∣V ∣  = 44, ∣ A ∣  = 78. (b) The corresponding GDI network with |V| = 44 and |A ′| = 666. Figure S4. Visualization of the GMI and the corresponding GDI networks in the case of HSN. (a) The GMI network with ∣V ∣  = 1609, ∣ A ∣  = 5063. (b) The corresponding GDI network with |V| = 1609 and |A ′| = 21221. Figure S5. Relationship of the GDI value to the length of a shortest path in random networks. (a-c) Results of the random networks shuffled from AMRN, ABAN, and HSN, respectively. (d) Results of 250 BA random networks with ∣V ∣  = 50, ∣ A ∣  = 80. (e) Results of 250 BA random networks with ∣V ∣  = 50, ∣ A ∣  = 100. Figure S6. Relationship of the GDI value to the number of paths in random networks. (a-c) Results of the random networks shuffled from AMRN, ABAN, and HSN, respectively. (d) Results of 250 BA random networks with ∣V ∣  = 50, ∣ A ∣  = 80. (e) Results of 250 BA random networks with ∣V ∣  = 50, ∣ A ∣  = 100. Figure S7. Relationship of the GDI value to the number of feedback loops involving the gene pair. Relationship of the GDI value to the number of feedback loops involving the gene pair. (a-c) Results of AMRN, ABAN, and HSN, respectively. (d-f) Results of the random networks shuffled from AMRN, ABAN, and HSN, respectively. Table S1. AMRN dataset consisting of 10 nodes and 20 interactions after removing self-loops from the original dataset. It includes the information about gene name as source and target, and interaction type. Table S2. ABAN dataset consisting of 44 nodes and 78 interactions after removing self-loops from the original dataset. It consists the information about gene name as source and target, and interaction type. Table S3. HSN dataset consisting of 1609 nodes and 5063 interactions after removing self-loops from the original dataset. It consists the information about gene name as source and target, and interaction type. Table S4. Information of drug-targets and side-effects for genes in HSN. It includes information about drug-targets and side-effects genes in HSN. (PDF 4490 kb