BioPlexPy

BioPlexPy provides programmatic access to protein-protein interaction (PPI) networks from the BioPlex project, including cell-line-specific datasets for 293T (~120,000 interactions among 15,000 proteins) and HCT116 (~70,000 interactions among 10,000 proteins), to support proteomics and integrative omics analyses.

Key Features:

• Access to BioPlex PPI networks: Programmatic retrieval of cell-line-specific PPI data derived from the BioPlex project for 293T and HCT116 cells.
• Cell-line interaction statistics: Includes dataset-level counts specifying ~120,000 interactions among 15,000 proteins for 293T and ~70,000 interactions among 10,000 proteins for HCT116.
• Integration with external biological resources: Provides access to CORUM protein complex annotations, PFAM protein domain information, and 3D structures from the Protein Data Bank (PDB).
• Transcriptome and proteome datasets: Bundles transcriptomic and proteomic measurements for the two cell lines to enable cross-omics analyses.
• R and Python interoperability: Interfaces programmatically with R and Python environments to support downstream computational analyses.
• Support for integrative analyses: Enables downstream computations such as maximum scoring sub-network analysis, protein domain–domain association studies, and mapping PPIs onto 3D structures.

Scientific Applications:

• Proteome network characterization: Analyze the functional organization of proteomes in 293T and HCT116 through cell-line-specific PPI networks.
• Network-based module detection: Apply maximum scoring sub-network analysis to identify high-scoring protein modules within PPI networks.
• Domain association studies: Investigate protein domain–domain associations using PFAM annotations mapped to PPIs.
• Structural mapping of interactions: Map PPIs onto 3D structures from the PDB to examine interaction interfaces and structural context.
• Integrative transcriptome–proteome analysis: Examine interactions at the interface of transcriptomic and proteomic datasets to study regulation and protein-level effects.

Methodology:

Programmatic retrieval of BioPlex PPI networks and associated CORUM, PFAM, PDB, transcriptome, and proteome datasets, with support for downstream analyses including maximum scoring sub-network analysis, protein domain–domain association studies, and mapping PPIs onto 3D structures.