A review on the computational approaches for gene regulatory network construction

Comput Biol Med. 2014 May;48:55-65. doi: 10.1016/j.compbiomed.2014.02.011. Epub 2014 Feb 24.

Abstract

Many biological research areas such as drug design require gene regulatory networks to provide clear insight and understanding of the cellular process in living cells. This is because interactions among the genes and their products play an important role in many molecular processes. A gene regulatory network can act as a blueprint for the researchers to observe the relationships among genes. Due to its importance, several computational approaches have been proposed to infer gene regulatory networks from gene expression data. In this review, six inference approaches are discussed: Boolean network, probabilistic Boolean network, ordinary differential equation, neural network, Bayesian network, and dynamic Bayesian network. These approaches are discussed in terms of introduction, methodology and recent applications of these approaches in gene regulatory network construction. These approaches are also compared in the discussion section. Furthermore, the strengths and weaknesses of these computational approaches are described.

Keywords: Bayesian network; Boolean network; Computational approaches; Dynamic Bayesian network; Gene expression data; Gene regulatory network; Neural network; Ordinary differential equation; Probabilistic Boolean network.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Algorithms
  • Bayes Theorem
  • Computational Biology / methods*
  • Gene Regulatory Networks*
  • Neural Networks, Computer