# PEANUT: Pathway Enrichment Analysis through Network UTilization

## TL;DR

PEANUT is a web-based tool that improves pathway enrichment analysis by using protein–protein interaction networks to detect relevant biological pathways more effectively.

## Contribution

PEANUT introduces network propagation in pathway enrichment analysis to enhance pathway detection using protein–protein interaction networks.

## Key findings

- PEANUT improves the detection of relevant pathways by amplifying signals through protein–protein interaction networks.
- The tool is accessible as an open-source web application with publicly available source code and a DOI for reproducibility.

## Abstract

Pathway enrichment analysis is a fundamental technique in bioinformatics for interpreting gene expression data to pinpoint biological pathways associated with specific conditions or diseases. We introduce Pathway Enrichment Analysis through Network UTilization (PEANUT), a web-based tool for pathway enrichment analysis that enhances traditional pipelines by integrating network propagation computations within a network of protein–protein interactions (PPIs). By diffusing gene expression scores through the PPI network, PEANUT amplifies the signals of connected sets of genes, thereby improving the detection of relevant pathways.

The tool is accessible as an open-source web application at https://peanut.cs.tau.ac.il/. The source code is available at https://github.com/Yapibe/PEANUT with a permanent identifier (DOI: https://doi.org/10.5281/zenodo.15184862).