Table 1.

Gene network analysis tools used in bioinformatics research studies.

Network Analysis Tool	Description
ARCANE	A tool for inferring gene regulatory networks from gene expression data. It employs mutual information-based methods to identify direct regulatory relationships.
WGCNA (Weighted Gene Co-Expression Network Analysis)	Used to identify co-expression modules within large gene expression datasets. It helps uncover gene networks related to specific biological processes or conditions.
GeneMANIA	A tool integrates various data sources to predict and visualize gene function and interactions. It helps users understand the functional relationships between genes in the context of specific biological processes.
VisANT	Network visualization and analysis tool that enables the exploration of biological pathways, gene interactions, and molecular networks
BioGRID	Offers tools for network analysis. It helps users explore physical and genetic interactions within a network context.
NetworkAnalyst	Integrated platform for network-based analysis that supports various types of omics data. It provides tools for network visualization, enrichment analysis, and pathway analysis.
RegulatoryNetworks	Focuses on the reconstruction and analysis of gene regulatory networks. It utilizes transcription factor binding site data to infer regulatory interactions.
GRNsight	Web-based tool for visualizing and analyzing gene regulatory networks. It helps users explore transcriptional interactions and regulatory relationships.
CytoScape.js	JavaScript library for network visualization that can be integrated into web applications to display and analyze gene networks interactively.
PathVisio	Offers plugins for network analysis. It allows users to draw, edit, and analyze biological pathways and networks.