CoExp: A Web Tool for the Exploitation of Co-expression Networks

Area of Science:

• Bioinformatics
• Computational Biology
• Systems Biology

Background:

• Gene co-expression networks (GCNs) are vital for understanding gene function and cellular specificity through transcriptomic profiling.
• Weighted Gene Co-expression Network Analysis (WGCNA) is a popular R package for constructing these networks.
• Analyzing multiple GCNs from diverse datasets is challenging due to a lack of integrated software tools.

Purpose of the Study:

• To introduce CoExp Web, a user-friendly web application for managing and exploring large collections of GCNs.
• To provide access to 109 pre-built co-expression networks from the CoExpNets R package suite.
• To enable researchers to build, manage, publish, and share their own GCNs.

Main Methods:

• Development of a web-based platform integrating the CoExpNets R package suite.
• Implementation of user-friendly interfaces for network exploration and gene annotation.
• Provision of open-source code for community use and custom GCN suite creation.

Main Results:

• CoExp Web offers a centralized platform for accessing and analyzing 109 GCNs.
• The application facilitates the annotation of genes of interest across various network models.
• The CoExpNets R packages and CoExp Web application are publicly available for community use.

Conclusions:

• CoExp Web significantly enhances the accessibility and usability of GCNs for biological research.
• The platform empowers researchers to integrate and analyze transcriptomic data more effectively.
• The open-source nature of the tools promotes collaborative GCN development and data sharing.