ArticleBMC proceedings2011
Constraint-based analysis of gene interactions using restricted boolean networks and time-series data.
Article in BMC proceedings, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- Identification of Boolean Network Models From Time Series Data Incorporating Prior Knowledge.Frontiers in physiology · 2018Article
- Construction and analysis of gene-gene dynamics influence networks based on a Boolean model.BMC systems biology · 2017Article
- Uncovering heterogeneous interactions in online commercial networks.Scientific reports · 2017Article
- Learning restricted Boolean network model by time-series data.EURASIP journal on bioinformatics & systems biology · 2014Article
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Authors and funding
4 authors.
Funding
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Abstract
backgroundA 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.
resultsWe 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.
conclusionsThe 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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