CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores

TL;DR

CytoSaddleSum is a Cytoscape plugin that enables functional enrichment analysis using SaddleSum, providing interactive network visualizations and easy integration into data workflows.

Contribution

It introduces a Cytoscape plugin that integrates SaddleSum's sum-of-weights enrichment analysis directly into network visualization workflows.

Findings

Enables local and remote SaddleSum queries within Cytoscape.

Displays enrichment results as interactive term relationship networks.

Allows saving and integrating results into Cytoscape workflows.

Abstract

Summary: CytoSaddleSum provides Cytoscape users with access to the functionality of SaddleSum, a functional enrichment tool based on sum-of-weight scores. It operates by querying SaddleSum locally (using the standalone version) or remotely (through an HTTP request to a web server). The functional enrichment results are shown as a term relationship network, where nodes represent terms and edges show term relationships. Furthermore, query results are written as Cytoscape attributes allowing easy saving, retrieval and integration into network-based data analysis workflows. Availability: www.ncbi.nlm.nih.gov/CBBresearch/Yu/downloads The source code is placed in Public Domain.