An overview of recent applications of Game Theory to bioinformatics

Game-theoretic link relevance indexing on genome-wide expression dataset identifies putative salient genes with potential etiological and diapeutics role in colorectal cancer

Diapeutics gene markers in colorectal cancer (CRC) can help manage mortality caused by the disease. We applied a game-theoretic link relevance Index (LRI) scoring on the high-throughput whole-genome transcriptome dataset to identify salient genes in CRC and obtained 126 salient genes with LRI score greater than zero. The biomarkers database lacks preliminary information on the salient genes as biomarkers for all the available cancer cell types. The salient genes revealed eleven, one and six overrepresentations for major Biological Processes, Molecular Function, and Cellular components. However, no enrichment with respect to chromosome location was found for the salient genes. Significantly high enrichments were observed for several KEGG, Reactome and PPI terms. The survival analysis of top protein-coding salient genes exhibited superior prognostic characteristics for CRC. MIR143HG, AMOTL1, ACTG2 and other salient genes lack sufficient information regarding their etiological role in CRC. Further investigation in LRI methodology and salient genes to augment the existing knowledge base may create new milestones in CRC diapeutics.

SEGN: Inferring real-time gene networks mediating phenotypic plasticity

The capacity of an organism to alter its phenotype in response to environmental perturbations changes over developmental time and is a process determined by multiple genes that are co-expressed in intricate but organized networks. Characterizing the spatiotemporal change of such gene networks can offer insight into the genomic signatures underlying organismic adaptation, but it represents a major methodological challenge. Here, we integrate the holistic view of systems biology and the interactive notion of evolutionary game theory to reconstruct so-called systems evolutionary game networks (SEGN) that can autonomously detect, track, and visualize environment-induced gene networks along the time axis. The SEGN overcomes the limitations of traditional approaches by inferring context-specific networks, encapsulating bidirectional, signed, and weighted gene-gene interactions into fully informative networks, and monitoring the process of how networks topologically alter across environmental and developmental cues. Based on the design principle of SEGN, we perform a transcriptional plasticity study by culturing Euphrates poplar, a tree that can grow in the saline desert, in saline-free and saline-stress conditions. SEGN characterize previously unknown gene co-regulation that modulates the time trajectories of the trees' response to salt stress. As a marriage of multiple disciplines, SEGN shows its potential to interpret gene interdependence, predict how transcriptional co-regulation responds to various regimes, and provides a hint for exploring the mass, energetic, or signal basis that drives various types of gene interactions.

Game theoretic centrality: a novel approach to prioritize disease candidate genes by combining biological networks with the Shapley value

Background

Complex human health conditions with etiological heterogeneity like Autism Spectrum Disorder (ASD) often pose a challenge for traditional genome-wide association study approaches in defining a clear genotype to phenotype model. Coalitional game theory (CGT) is an exciting method that can consider the combinatorial effect of groups of variants working in concert to produce a phenotype. CGT has been applied to associate likely-gene-disrupting variants encoded from whole genome sequence data to ASD; however, this previous approach cannot take into account for prior biological knowledge. Here we extend CGT to incorporate a priori knowledge from biological networks through a game theoretic centrality measure based on Shapley value to rank genes by their relevance–the individual gene’s synergistic influence in a gene-to-gene interaction network. Game theoretic centrality extends the notion of Shapley value to the evaluation of a gene’s contribution to the overall connectivity of its corresponding node in a biological network.

Results

We implemented and applied game theoretic centrality to rank genes on whole genomes from 756 multiplex autism families. Top ranking genes with the highest game theoretic centrality in both the weighted and unweighted approaches were enriched for pathways previously associated with autism, including pathways of the immune system. Four of the selected genes HLA-A, HLA-B, HLA-G, and HLA-DRB1–have also been implicated in ASD and further support the link between ASD and the human leukocyte antigen complex.

Conclusions

Game theoretic centrality can prioritize influential, disease-associated genes within biological networks, and assist in the decoding of polygenic associations to complex disorders like autism.

Quantum Conditional Strategies and Automata for Prisoners’ Dilemmata under the EWL Scheme

Classical game theory is an important field with a long tradition of useful results. Recently, the quantum versions of classical games, such as the prisoner’s dilemma (PD), have attracted a lot of attention. This game variant can be considered as a specific type of game where the player’s actions and strategies are formed using notions from quantum computation. Similarly, state machines, and specifically finite automata, have also been under constant and thorough study for plenty of reasons. The quantum analogues of these abstract machines, like the quantum finite automata, have been studied extensively. In this work, we examine well-known conditional strategies that have been studied within the framework of the classical repeated PD game. Then, we try to associate these strategies to proper quantum finite automata that receive them as inputs and recognize them with a probability of 1, achieving some interesting results. We also study the quantum version of PD under the Eisert–Wilkens–Lewenstein scheme, proposing a novel conditional strategy for the repeated version of this game.

Solving Potential Games With Dynamical Constraint

We solve N -player potential games with dynamical constraint in this paper. Potential games with stable dynamics are first considered followed by one type of potential games without inherently stable dynamics. Different from most of the existing Nash seeking methods, we provide an extremum seeking-based method that does not require explicit information on the game dynamics or the payoff functions. Only measurements of the payoff functions are needed in the game strategy synthesis. Lie bracket approximation is used for the analysis of the proposed Nash seeking scheme. A singularly semi-globally practically uniformly asymptotically stable result is presented for potential games with stable dynamics and an ultimately bounded result is provided for potential games without inherently stable dynamics. For first-order perturbed integrator-type dynamics, we employ an extended-state observer to deal with the disturbance such that better convergence is achievable. Stability of the closed-loop system is proven and the ultimate bound is quantified. Numerical examples are presented to verify the effectiveness of the proposed methods.