ترغب بنشر مسار تعليمي؟ اضغط هنا

Mutual information in random Boolean models of regulatory networks

84   0   0.0 ( 0 )
 نشر من قبل Joshua E. S. Socolar
 تاريخ النشر 2007
  مجال البحث علم الأحياء
والبحث باللغة English




اسأل ChatGPT حول البحث

The amount of mutual information contained in time series of two elements gives a measure of how well their activities are coordinated. In a large, complex network of interacting elements, such as a genetic regulatory network within a cell, the average of the mutual information over all pairs <I> is a global measure of how well the system can coordinate its internal dynamics. We study this average pairwise mutual information in random Boolean networks (RBNs) as a function of the distribution of Boolean rules implemented at each element, assuming that the links in the network are randomly placed. Efficient numerical methods for calculating <I> show that as the number of network nodes N approaches infinity, the quantity N<I> exhibits a discontinuity at parameter values corresponding to critical RBNs. For finite systems it peaks near the critical value, but slightly in the disordered regime for typical parameter variations. The source of high values of N<I> is the indirect correlations between pairs of elements from different long chains with a common starting point. The contribution from pairs that are directly linked approaches zero for critical networks and peaks deep in the disordered regime.

قيم البحث

اقرأ أيضاً

Random Boolean networks are models of disordered causal systems that can occur in cells and the biosphere. These are open thermodynamic systems exhibiting a flow of energy that is dissipated at a finite rate. Life does work to acquire more energy, th en uses the available energy it has gained to perform more work. It is plausible that natural selection has optimized many biological systems for power efficiency: useful power generated per unit fuel. In this letter we begin to investigate these questions for random Boolean networks using Landauers erasure principle, which defines a minimum entropy cost for bit erasure. We show that critical Boolean networks maximize available power efficiency, which requires that the system have a finite displacement from equilibrium. Our initial results may extend to more realistic models for cells and ecosystems.
Network of packages with regulatory interactions (dependences and conflicts) from Debian GNU/Linux operating system is compiled and used as analogy of a gene regulatory network. Using a trace-back algorithm we assembly networks from the potential poo l of packages for both scale-free and exponential topology from real and a null model data, respectively. We calculate the maximum number of packages that can be functionally installed in the system (i.e., the active network size). We show that scale-free regulatory networks allow a larger active network size than random ones. Small genomes with scale-free regulatory topology could allow much more functionality than large genomes with an exponential one, with implications on its dynamics, robustness and evolution.
Boolean networks have long been used as models of molecular networks and play an increasingly important role in systems biology. This paper describes a software package, Polynome, offered as a web service, that helps users construct Boolean network m odels based on experimental data and biological input. The key feature is a discrete analog of parameter estimation for continuous models. With only experimental data as input, the software can be used as a tool for reverse-engineering of Boolean network models from experimental time course data.
We study a class of growth algorithms for directed graphs that are candidate models for the evolution of genetic regulatory networks. The algorithms involve partial duplication of nodes and their links, together with innovation of new links, allowing for the possibility that input and output links from a newly created node may have different probabilities of survival. We find some counterintuitive trends as parameters are varied, including the broadening of indegree distribution when the probability for retaining input links is decreased. We also find that both the scaling of transcription factors with genome size and the measured degree distributions for genes in yeast can be reproduced by the growth algorithm if and only if a special seed is used to initiate the process.
Objectives: A conflicting body of evidence suggests localized periodontal inflammation to spread systemically during pregnancy inducing adverse pregnancy outcomes. This systematic review and meta-analysis aimed to specifically evaluate the relationsh ip between periodontitis and preeclampsia. Methods: Electronic searches were carried out in Medline, Pubmed, Cochrane Controlled Clinical Trial Register to identify and select observational case-control and cohort studies that analyzed the association between periodontal disease and preeclampsia. Prisma guidelines and Moose checklist were followed. Results: Thirty studies including six cohorts and twenty-four case-control studies were selected. Periodontitis was significantly associated with increased risk for preeclampsia, especially in a subgroup analysis including cohort studies and subgroup analysis with lower-middle-income countries. Conclusion: Periodontitis appears as a significant risk factor for preeclampsia, which might be even more pronounced in lower-middle-income countries.
التعليقات
جاري جلب التعليقات جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
mircosoft-partner

هل ترغب بارسال اشعارات عن اخر التحديثات في شمرا-اكاديميا