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

BMC Proceedings
Carlos H A HigaRonaldo F Hashimoto

Abstract

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. 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. 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.

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Citations

Jun 1, 2011·BMC Proceedings·Marcin PszczolaMaciej Szydlowski
May 25, 2013·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Carlos H A HigaRonaldo F Hashimoto
Aug 6, 2014·EURASIP Journal on Bioinformatics & Systems Biology·Hongjia OuyangWenbin Liu
Dec 10, 2017·Scientific Reports·Fangfeng ZhangZengru Di
Jan 13, 2018·BMC Systems Biology·Maulida MazayaYung-Keun Kwon
Jun 26, 2018·Frontiers in Physiology·Thomas LeifeldPing Zhang

Related Concepts

Gene Expression
Genes
HeLa Cells
Physiological Aspects
Satisfaction
Gene Interaction
Research Study
Analysis
Cell Budding
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