BioPlex: An Integrated Data Product For The Analysis Of Human Protein-Protein Interactions
Author(s): Ludwig Geistlinger, Roger Vargas, Joshua Pan, Edward Huttlin, Robert Gentleman
Affiliation(s): Center for Computational Biomedicine
Summary: The BioPlex project has created two proteome-scale, cell-line-specific protein-protein interaction (PPI) networks: the first in 293T cells, including 120k interactions among 15k proteins; and the second in HCT116 cells, including 70k interactions between 10k proteins. Here, we describe programmatic access to the BioPlex PPI networks and integration with related resources from within R and Python. Besides PPI networks for 293T and HCT116 cells, this includes access to CORUM protein complex data, PFAM protein domain data, PDB protein structures, and transcriptome and proteome data for the two cell lines. The implemented functionality serves as a basis for integrative downstream analysis of BioPlex PPI data with domain-specific R and Python packages, including efficient execution of maximum scoring subnetwork analysis, protein domain-domain association analysis, mapping of PPIs onto 3D protein structures, and analysis of BioPlex PPIs at the interface of transcriptomic and proteomic data. Availability and implementation: http://bioconductor.org/packages/BioPlex https://github.com/ccb-hms/BioPlexAnalysis https://github.com/ccb-hms/BioPlexPy