MDA231_specific_PPI>=0.9

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.