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Development and use of a Cytoscape app for GRNCOP2
Juan J Díaz-Montaña1, Norberto Díaz-Díaz1, Carlos D Barranco1
1Intelligent Data Analysis (DATAi), Division of Computer Science, Pablo de Olavide University, Seville ES-41013, Spain.
Computer Methods and Programs in Biomedicine
|July 20, 2019
Summary
A new Cytoscape app integrates GRNCOP2 for gene regulatory network analysis. This tool aids in understanding complex biological pathways and disease progression, like Alzheimer's disease, by visualizing and analyzing network data.
Area of Science:
- Systems Biology
- Bioinformatics
- Computational Biology
Background:
- Gene regulatory networks (GRNs) are crucial for understanding molecular processes.
- Model-free approaches, like GRNCOP2, excel at modeling complex GRN topologies.
- GRNCOP2 offers efficient data-driven analysis with minimal data requirements.
Purpose of the Study:
- To integrate GRNCOP2 into the Cytoscape ecosystem for enhanced network visualization and analysis.
- To leverage Cytoscape's capabilities for interactive exploration of GRNs.
- To facilitate topological analysis of complex gene association networks.
Main Methods:
- Developed a Cytoscape app for GRNCOP2.
- Implemented new functionalities for GRN visualization and user interaction.
- Integrated with other Cytoscape apps for advanced topological analysis.
Main Results:
- Demonstrated the app's utility through a novel use case: analyzing pathway crosstalk.
- Analyzed Alzheimer's disease datasets to understand progression and synchronization with the Ubiquitin Mediated Proteolysis pathway.
- Evaluated the biological relevance of findings through literature review.
Conclusions:
- The GRNCOP2 Cytoscape app enables assessment of disease progression phases and identification of signaling genes.
- Topological contrastive analysis within Cytoscape revealed insights into cellular process coordination.
- Inferred topological patterns align with existing biological evidence, confirming the app's effectiveness.
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