BioPlex

BioPlex provides programmatic access to proteome-scale protein-protein interaction (PPI) networks for the 293T and HCT116 cell lines to support analysis of cellular interaction networks.

Key Features:

• Cell-line-specific networks: PPI networks for 293T (approximately 120,000 interactions among 15,000 proteins) and HCT116 (around 70,000 interactions between 10,000 proteins).
• Programmatic access and language support: Programmatic access within R with support for integration into Python workflows.
• Resource integration: Integration with CORUM protein complex data, PFAM protein domain information, PDB structures, and transcriptome/proteome datasets for the two cell lines.
• Analytical capabilities: Enables maximum scoring sub-network analysis, protein domain–domain association analysis, mapping of PPIs onto three-dimensional structures, and transcriptomic–proteomic interface analysis.

Scientific Applications:

• Systems biology investigations: Proteome-scale network analysis to study cellular mechanisms and interaction topology.
• Target discovery: Identification and prioritization of candidate therapeutic targets based on network context and sub-network scoring.
• Protein function and interaction dynamics: Exploration of protein domain associations, structural mapping of interfaces, and integration with transcriptomic and proteomic data to infer functional relationships.

Methodology:

Programmatic access within R with integration into R and Python tools to perform integrative downstream analyses combining PPI data with domain-specific tools, including maximum scoring sub-network analysis, protein domain–domain association analysis, mapping PPIs onto 3D structures, and transcriptomic–proteomic interface analysis.