Finding the fixed points of a Boolean network from a positive feedback vertex set.
Julio Aracena1, Luis Cabrera-Crot2, Lilian Salinas2
1CI2MA and Departamento de Ingeniería Matemática, Facultad de Ciencias Físicas y Matemáticas, Universidad de Concepción, Concepción, Chile.
Bioinformatics (Oxford, England)
|November 2, 2020
Summary
This study introduces a novel algorithm for identifying fixed points in Boolean networks, considering regulatory graph properties. The new method efficiently finds fixed points by incorporating positive feedback vertex sets, improving upon existing approaches.
Area of Science:
- Computational Biology
- Systems Biology
- Bioinformatics
Background:
- Boolean networks are crucial for modeling biological systems.
- Identifying fixed points is a key challenge in Boolean network analysis.
- Existing algorithms often overlook the influence of activation/inhibition types.
Purpose of the Study:
- To develop a new algorithm for finding fixed points in Boolean networks.
- To address limitations of previous methods by incorporating regulatory graph properties.
- To provide a theoretical characterization of Boolean networks with fixed points and no positive cycles.
Main Methods:
- The proposed algorithm utilizes a positive feedback vertex set (P) of the regulatory graph.
- It employs a sequential update schedule for network components.
- The algorithm's runtime complexity is O(2|P|·n^2+k).
Main Results:
- A novel algorithm for Boolean network fixed point identification is presented.
- The algorithm's efficiency is dependent on the size of the positive feedback vertex set.
- Theoretical insights into the dynamics of Boolean networks without positive cycles are provided.
Conclusions:
- The new algorithm offers an improved approach to finding fixed points in Boolean networks.
- It provides a more comprehensive analysis by considering regulatory interactions.
- The algorithm is implemented in Java and available for use.
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