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Bioinformatics Advance Access published online on November 5, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti131
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received September 16, 2004
Revised October 31, 2004
Accepted November 1, 2004

Article

Intervention in context-sensitive probabilistic boolean networks

Ranadip Pal 1, Aniruddha Datta 1, Michael L. Bittner 2, and Edward R. Dougherty 3*

1 Department of Electrical Engineering, Texas A&M University, College Station, TX, 77843, USA
2 Translational Genomics Research Institute, 400 North Fifth Street, Suite 1600, Phoenix, AZ 85004, USA
3 Department of Electrical Engineering, Texas A&M University, College Station, TX, 77843, USA; University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA

* To whom correspondence should be addressed.
Edward R. Dougherty, E-mail: edward{at}ee.tamu.edu


  Abstract

Motivation: Intervention in a gene regulatory network is used to help it avoid undesirable states, such as those associated with a disease. Several types of intervention have been studied in the framework of a probabilistic Boolean network (PBN), which is essentially a finite collection of Boolean networks in which at any discrete time point the gene state vector transitions according to the rules of one of the constituent networks. For an instantaneously random PBN, the governing Boolean network is randomly chosen at each time point. For a context-sensitive PBN, the governing Boolean network remains fixed for an interval of time until a binary random variable determines a switch. The theory of automatic control has been previously applied to find optimal strategies for manipulating external (control) variables that affect the transition probabilities of an instantaneously random PBN to desirably affect its dynamic evolution over a finite time horizon. This paper extends the methods of external control to context-sensitive PBNs.

Results: This paper treats intervention via external control variables in context-sensitive PBNs by extending the results for instantaneously random PBNs in several directions. First, and most importantly, whereas an instantaneously random PBN yields a Markov chain whose state space is composed of gene vectors, each state of the Markov chain corresponding to a context-sensitive PBN is composed of a pair, the current gene vector occupied by the network and the current constituent Boolean network. Second, the analysis is applied to PBNs with perturbation, meaning that random gene perturbation is permitted at each instant with some probability. Third, the (mathematical) influence of genes within the network is used to choose the particular gene with which to intervene. Lastly, PBNs are designed from data using a recently proposed inference procedure that takes steady-state considerations into account. The results are applied to a context-sensitive PBN derived from gene-expression data collected in a study of metastatic melanoma, the intent being to devise a control strategy that reduces the WNT5A gene's action in affecting biological regulation, since the available data suggests that disruption of this influence could reduce the chance of a melanoma metastasizing.


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