SIREN Cytoscape plugin: Interaction Type Discrimination in Gene Regulatory Networks

TL;DR

SIREN is a Cytoscape plugin that uses information theory to quickly and efficiently determine whether gene interactions are activating or inhibitory based on expression data, aiding in understanding gene regulatory networks.

Contribution

The paper introduces SIREN, a novel, fast, and memory-efficient Java plugin for Cytoscape that discriminates interaction types in gene regulatory networks using expression data.

Findings

SIREN accurately predicts interaction types in gene networks.

The tool is computationally efficient and easy to integrate.

It enhances network analysis by providing interaction nature insights.

Abstract

Integrating expression data with gene interactions in a network is essential for understanding the functional organization of the cells. Consequently, knowledge of interaction types in biological networks is important for data interpretation. Signing of Regulatory Networks (SIREN) plugin for Cytoscape is an open-source Java tool for discrimination of interaction type (activatory or inhibitory) in gene regulatory networks. Utilizing an information theory based concept, SIREN seeks to identify the interaction type of pairs of genes by examining their corresponding gene expression profiles. We introduce SIREN, a fast and memory efficient tool with low computational complexity, that allows the user to easily consider it as a complementary approach for many network reconstruction methods. SIREN allows biologists to use independent expression data to predict interaction types for known gene regulatory networks where reconstruction methods do not provide any information about the nature of their interaction types. The SIREN Cytoscape plugin is implemented in Java and is freely available at http://baderlab.org/Software/SIRENplugin and via the Cytoscape app manager.