Breast cancer protein-protein interaction network

Interactome of the union of all high-confidence PPIs detected across three breast cell lines (MCF7, MDA-MB-231, and MCF10A). In this network, PPIs from wild-type and mutant isoforms of each bait were combined. Edges are colored based on their differential interaction, with pink edges representing PPIs that are enriched to BC cell lines (unique to either MDA-MB-231 or MCF7) as compared to MCF10A cells (shown in teal edges). Baits are shown as yellow box, and preys as grey circle. Size of each node represents number of patients with alterations in each protein. Dotted line represents the physical protein-protein association (validated in other studies) with high Integrated Association Stringency score. 
We developed a method for calculating a differential interaction score (DIS) and a corresponding false discovery rate (FDR) using AP-MS data across multiple cell lines. This approach uses the SAINTexpress score (Teo et al., 2014b) which is the probability of a PPI being bonafide in a single cell line computed using a mixture of distribution modeling spectral counts of true and false interactions. The probabilities based on the analysis of a single cell line can then be used to calculate a differential interaction score between PPIs present in cancer cells and normal cells. We define a cancer-specific differential interaction score as the probability of the PPI being present in a cancer cell line but absent in the normal cell line.