It indicates that all four models show attractor stability. serotonin reuptake inhibitors (SSRIs), in order to observe how the pathways interact and to examine if the system is stable. Additionally, we wanted to study which genes or metabolites have the greatest impact on model stability when knocked out strain K-12 [28]. Furthermore, this ST 101(ZSET1446) approach has also been applied to search for new candidate genes in schizophrenia [21] and as a modeling technique in cancer studies [29]. The aim of this work was to use a Boolean approximation to analyze an integrated network involving the 5-HT neurotransmitter pathway, neurotrophin signaling and the HPA cortisol synthesis pathway in the presence and absence of stress and serotonin ST 101(ZSET1446) selective reuptake inhibitors (SSRIs). We also evaluated network stability and the effects that knocked-out genes had on the network to search for probable candidate genes involved in MDD. Methods The Methods section is depicted in Figure?1 to clarify the methodology used. Open in a separate window Figure 1 A flow chart illustrating the methodology used to model the network. For more information, refer to the Methods section. Model definition and network simulation The biological information used to generate the network is shown in Appendix A and was analyzed using an SBN approximation. The model was simulated using the Random Boolean Networks (RBN) toolbox (free download at http://www.teuscher.ch/rbntoolbox) for Matlab? by using the tools that allow for well-defined connections among nodes. Boolean logic was applied to identify the logic operators (AND and AND-NOT) that allow the model to simulate the network [30]. The Boolean simplification gave 41 nodes that were logically connected and allowed the construction of a rules-matrix, which defines the logic transition rules for each node in the network, and a connection-matrix, which explains the connectivity of the nodes. Both matrixes are in conjunction the mathematical model behind the simulations performed. The rules-matrix size was 2kxN (N nodes and k connections). Each node has k possible entrances that only generate two responses (1 or 0 for ST 101(ZSET1446) on or off, respectively). Our network has 41 nodes and up to 4 entrances with a rules-matrix size of 24×41. Each column of this matrix is created using 41 different matrices, where each of these matrices holds the response of each node according to the 4 different binary organized entrances. The connection-matrix created has a size of NxN where each of the matrix entrances (i,j) defines the number of connections from node i to node j with a column sum restriction equal to k. The initial states for all nodes were set to 1 1 (on) for every node in the network except for the nodes corresponding to stress and to SSRI, which Rabbit polyclonal to FBXO10 were permuted between 1 and 0 (on or off). Therefore, four initial states were generated: 1) Basal Model: all 41 nodes initially active except the stress and SSRI nodes, 2) Antidepressant Model: all 41 nodes active except the stress node, 3) Chronic Stress Model: all 41 nodes active except the SSRI node and 4) Complete Model: all 41 nodes active. In our model, the stress, tryptophan (TRP) and selective serotonin reuptake inhibitor (SSRI) nodes remain in a steady state throughout the simulations because they are not downregulated by any other node. To verify that the network was stable, attractors were obtained from each simulation. The simulations performed are shown in Figure?1. Each of the four simulations were performed in a 2.8GHz Intel Core 2 Duo with 4GB RAM, taking ~5?s per run. Stability analysis through knockouts knockouts were generated for all nodes and their effects on.
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