PEANUT

PEANUT (Pathway Enrichment Analysis through Network Utilization) is a next-generation web server for pathway enrichment analysis. By integrating network propagation techniques into Protein-Protein Interaction (PPI) networks, PEANUT enhances the detection of biologically significant pathways, outperforming traditional methods in both sensitivity and accuracy. This tool provides researchers with a novel way to identify pathways associated with specific gene expression profiles, leveraging the inherent connectivity within biological networks.

How PEANUT Works:

PEANUT uses network propagation to diffuse gene expression scores across the PPI network. This process amplifies the signals of interconnected genes, improving the detection of pathways that might be overlooked in traditional enrichment methods.

Key Features:

• Simultaneous Analysis: Run multiple conditions or datasets simultaneously, allowing for direct comparisons of results across conditions or methods. Furthermore, GSEA and PEANUT analyses can be executed side-by-side to easily compare their outputs.
• Propagation Alpha: Control the depth of network propagation. Higher alpha values prioritize immediate interactions, while lower values enable a broader exploration of the network.
• Custom Pathway Analysis: Import pre-ranked gene lists to tailor the analysis to specific datasets or hypotheses. Results include pathway ranks, statistical scores, and detailed visualizations.
• Open Access: PEANUT is freely accessible online, designed for researchers across disciplines, and compatible with pre-ranked gene expression data from diverse biological studies.

Last updated: Aug 02, 2025