A full bayesian approach for boolean genetic network inference

PLoS One. 2014 Dec 31;9(12):e115806. doi: 10.1371/journal.pone.0115806. eCollection 2014.

Abstract

Boolean networks are a simple but efficient model for describing gene regulatory systems. A number of algorithms have been proposed to infer Boolean networks. However, these methods do not take full consideration of the effects of noise and model uncertainty. In this paper, we propose a full Bayesian approach to infer Boolean genetic networks. Markov chain Monte Carlo algorithms are used to obtain the posterior samples of both the network structure and the related parameters. In addition to regular link addition and removal moves, which can guarantee the irreducibility of the Markov chain for traversing the whole network space, carefully constructed mixture proposals are used to improve the Markov chain Monte Carlo convergence. Both simulations and a real application on cell-cycle data show that our method is more powerful than existing methods for the inference of both the topology and logic relations of the Boolean network from observed data.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Bayes Theorem
  • Cell Cycle / genetics
  • Computer Simulation
  • Gene Expression Regulation / genetics*
  • Gene Regulatory Networks / genetics*
  • Markov Chains
  • Models, Genetic*
  • Monte Carlo Method

Grants and funding

This research is partially supported by a grant from the Research Grants Council of the Hong Kong SAR (Project no. CUHK 400913), a CUHK direct grant (Project no. CUHK 2060419), a grant from the University Grants Committee of the Hong Kong Special Administrative Region, China (Project No. AoE/E-02/08), three grants from the National Science Foundation of USA (Grant No. 1007520, 1209226, and 1209232), and a grant from the National Basic Research Program of China (973 Program, No. 2012CB315901, No. 2012CB315904). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.