Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks

  • Authors:

  • Harri Lähdesmäki;Sampsa Hautaniemi;Ilya Shmulevich;Olli Yli-Harja

  • Affiliations:

  • Institute of Signal Processing, Tampere University of Technology, Tampere, Finland and Cancer Genomics Laboratory, The University of Texas M. D. Anderson Cancer Center, Houston, TX;Institute of Signal Processing, Tampere University of Technology, Tampere, Finland;Institute for Systems Biology, Seattle, WA;Institute of Signal Processing, Tampere University of Technology, Tampere, Finland

  • Venue:
  • Signal Processing
  • Year:
  • 2006

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Abstract

A significant amount of attention has recently been focused on modeling of gene regulatory networks. Two frequently used large-scale modeling frameworks are Bayesian networks (BNs) and Boolean networks, the latter one being a special case of its recent stochastic extension, probabilistic Boolean networks (PBNs). PBN is a promising model class that generalizes the standard rule-based interactions of Boolean networks into the stochastic setting. Dynamic Bayesian networks (DBNs) is a general and versatile model class that is able to represent complex temporal stochastic processes and has also been proposed as a model for gene regulatory systems. In this paper, we concentrate on these two model classes and demonstrate that PBNs and a certain subclass of DBNs can represent the same joint probability distribution over their common variables. The major benefit of introducing the relationships between the models is that it opens up the possibility of applying the standard tools of DBNs to PBNs and vice versa. Hence, the standard learning tools of DBNs can be applied in the context of PBNs, and the inference methods give a natural way of handling the missing values in PBNs which are often present in gene expression measurements. Conversely, the tools for controlling the stationary behavior of the networks, tools for projecting networks onto sub-networks, and efficient learning schemes can be used for DBNs. In other words, the introduced relationships between the models extend the collection of analysis tools for both model classes.