PPIExp: A Web-Based Platform for Integration and Visualization of Protein-Protein Interaction Data and Spatiotemporal...

Area of Science:

• Proteomics
• Bioinformatics
• Systems Biology

Background:

• Integrating spatiotemporal proteomics with protein-protein interaction (PPI) data enables dynamic exploration of protein functions.
• Biologists often lack programming skills, hindering their ability to construct and analyze PPI networks.

Purpose of the Study:

• To develop a user-friendly web-based platform, PPIExp, for constructing and visualizing PPI networks from spatiotemporal proteomics data.
• To facilitate the identification of key proteins and active subnetworks for further biological investigation.

Main Methods:

• PPIExp automatically constructs PPI networks and performs clustering based on protein abundances.
• It integrates functional enrichment analysis and offers multiple visualization interfaces (network map, dendrogram, heatmap, expression patterns).
• The platform highlights differentially expressed proteins and provides interactive tools to identify key nodes based on centrality and functional annotations.

Main Results:

• PPIExp provides automated PPI network construction and clustering analysis.
• It offers interactive visualization of PPI networks, clustering results, and protein expression patterns.
• The tool facilitates the identification of key proteins within enriched functional terms or coexpressed groups.

Conclusions:

• PPIExp empowers biologists with limited programming experience to analyze complex PPI networks and spatiotemporal proteomics data.
• The platform enhances the exploration of dynamic biological processes by simplifying network analysis and key protein identification.