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PEANUT: Pathway Enrichment Analysis through Network UTilization
Yair Pickholz Berliner1, Roded Sharan1
1School of Computer Science and AI, Tel Aviv University, Tel Aviv, 69978, Israel.
Bioinformatics (Oxford, England)
|July 22, 2025
Summary
We developed PEANUT, a novel bioinformatics tool for pathway enrichment analysis. It improves disease-gene association discovery by integrating gene expression data with protein-protein interaction networks.
Area of Science:
- Bioinformatics
- Computational Biology
- Systems Biology
Background:
- Pathway enrichment analysis is crucial for interpreting gene expression data.
- Identifying biological pathways linked to diseases aids in understanding disease mechanisms.
Purpose of the Study:
- Introduce PEANUT (Pathway Enrichment Analysis through Network UTilization), a web-based tool.
- Enhance traditional pathway enrichment analysis by incorporating network propagation.
Main Methods:
- Utilize a protein-protein interaction (PPI) network.
- Perform network propagation by diffusing gene expression scores.
- Amplify signals of connected gene sets within the PPI network.
Main Results:
- Improved detection of relevant biological pathways.
- Enhanced identification of gene sets associated with specific conditions.
- More sensitive pathway enrichment analysis.
Conclusions:
- PEANUT offers an advanced approach to pathway enrichment analysis.
- Integrating network propagation with gene expression data improves biological insight.
- The tool facilitates the discovery of condition-specific pathways.
