Pickholz Berliner Yair, Sharan Roded
School of Computer Science and AI, Tel Aviv University, Tel Aviv, 69978, Israel.
Bioinformatics. 2025 Jul 1;41(7). doi: 10.1093/bioinformatics/btaf410.
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).
通路富集分析是生物信息学中的一项基本技术，用于解释基因表达数据，以确定与特定条件或疾病相关的生物通路。我们介绍了通过网络利用进行通路富集分析（PEANUT），这是一种基于网络的通路富集分析工具，通过在蛋白质-蛋白质相互作用（PPI）网络中整合网络传播计算来增强传统流程。通过在PPI网络中扩散基因表达分数，PEANUT放大了相连基因集的信号，从而提高了相关通路的检测能力。
该工具可作为开源网络应用程序在https://peanut.cs.tau.ac.il/上访问。源代码可在https://github.com/Yapibe/PEANUT上获取，并具有永久标识符（DOI：https://doi.org/10.5281/zenodo.15184862）。
