Integrated Inference of Asymmetric Protein Interaction Networks Using Dynamic Model and Individual Patient Proteomics Data

“Mathematics and Symmetry/Asymmetry Section”—Editorial 2020–2021

As it is well known, the Mathematics and Symmetry/Asymmetry Section is one of the most active sections of the Symmetry journal [...]

Inference of Molecular Regulatory Systems Using Statistical Path-Consistency Algorithm

One of the key challenges in systems biology and molecular sciences is how to infer regulatory relationships between genes and proteins using high-throughout omics datasets. Although a wide range of methods have been designed to reverse engineer the regulatory networks, recent studies show that the inferred network may depend on the variable order in the dataset. In this work, we develop a new algorithm, called the statistical path-consistency algorithm (SPCA), to solve the problem of the dependence of variable order. This method generates a number of different variable orders using random samples, and then infers a network by using the path-consistent algorithm based on each variable order. We propose measures to determine the edge weights using the corresponding edge weights in the inferred networks, and choose the edges with the largest weights as the putative regulations between genes or proteins. The developed method is rigorously assessed by the six benchmark networks in DREAM challenges, the mitogen-activated protein (MAP) kinase pathway, and a cancer-specific gene regulatory network. The inferred networks are compared with those obtained by using two up-to-date inference methods. The accuracy of the inferred networks shows that the developed method is effective for discovering molecular regulatory systems.

Mathematical Modeling and Analysis of Tumor Chemotherapy

Cancer diseases lead to the second-highest death rate all over the world. For treating tumors, one of the most common schemes is chemotherapy, which can decrease the tumor size and control the progression of cancer diseases. To better understand the mechanisms of chemotherapy, we developed a mathematical model of tumor growth under chemotherapy. This model includes both immune system response and drug therapy. We characterize the symmetrical properties and dynamics of this differential equation model by finding the equilibrium points and exploring the stability and symmetry properties in a range of model parameters. Sensitivity analyses suggest that the chemotherapy drug-induced tumor mortality rate and the drug decay rate contribute significantly to the determination of treatment outcomes. Numerical simulations highlight the importance of CTL activation in tumor chemotherapy.