BioPlexAnalysis

Applications and downstream analysis of BioPlex PPI data

The BioPlex project uses affinity-purification mass spectrometry to profile protein-protein interactions (PPIs) in human cell lines.

To date, the BioPlex project has created two proteome-scale, cell-line-specific PPI networks. The first, BioPlex 3.0, results from affinity purification of 10,128 human proteins —- half the proteome —- in 293T cells and includes 118,162 interactions among 14,586 proteins. The second results from 5,522 immunoprecipitations in HCT116 cells and includes 70,966 interactions between 10,531 proteins.

For more information, please see:

• Huttlin et al. The BioPlex network: a systematic exploration of the human interactome. Cell, 2015.
• Huttlin et al. Architecture of the human interactome defines protein communities and disease networks, Nature, 2017.
• Huttlin et al. Dual proteome-scale networks reveal cell-specific remodeling of the human interactome, Cell, 2021.

The BioPlex R package implements access to the BioPlex protein-protein interaction networks and related resources from within R. Besides protein-protein interaction networks for 293T and HCT116 cells, this includes access to CORUM protein complex data, and transcriptome and proteome data for the two cell lines.

Functionality focuses on importing these data resources and storing them in dedicated Bioconductor data structures, as a foundation for integrative downstream analysis of the data. This repository contains code for a set of downstream analyses and applications of BioPlexPPI data, bundled in the BioPlexAnalysis R package and compiled analysis vignettes.