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This article is part of the supplement: Selected Proceedings of the 6th International Symposium on Bioinformatics Research and Applications (ISBRA'10)

Open Access Proceedings

Constraint-based analysis of gene interactions using restricted boolean networks and time-series data

Carlos HA Higa12, Vitor HP Louzada1, Tales P Andrade1 and Ronaldo F Hashimoto1*

Author Affiliations

1 Institute of Mathematics and Statistics, University of Sao Paulo, Rua do Matao 1010, 05508-090, Sao Paulo - SP, Brazil

2 School of Computing, Federal University of Mato Grosso do Sul, Cidade Universitaria, 79070-900, Campo Grande - MS, Brazil

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BMC Proceedings 2011, 5(Suppl 2):S5  doi:10.1186/1753-6561-5-S2-S5

Published: 28 April 2011

Abstract

Background

A popular model for gene regulatory networks is the Boolean network model. In this paper, we propose an algorithm to perform an analysis of gene regulatory interactions using the Boolean network model and time-series data. Actually, the Boolean network is restricted in the sense that only a subset of all possible Boolean functions are considered. We explore some mathematical properties of the restricted Boolean networks in order to avoid the full search approach. The problem is modeled as a Constraint Satisfaction Problem (CSP) and CSP techniques are used to solve it.

Results

We applied the proposed algorithm in two data sets. First, we used an artificial dataset obtained from a model for the budding yeast cell cycle. The second data set is derived from experiments performed using HeLa cells. The results show that some interactions can be fully or, at least, partially determined under the Boolean model considered.

Conclusions

The algorithm proposed can be used as a first step for detection of gene/protein interactions. It is able to infer gene relationships from time-series data of gene expression, and this inference process can be aided by a priori knowledge available.