FuzzyPPI: Human Proteome at Fuzzy Semantic Space

Large scale protein-protein interaction (PPI) network of an organism provides key insights into the cellular and molecular functionalities, signaling pathways and underlying disease mechanisms. If we consider the complete interactome of any given organism, the total number of unexplored protein interactions significantly outnumbers the known positive and negative interactions. For Human 20,350 reviewed proteins can generate over ~207 million potential interactions. However, the combination of all known PPI datasets, contains only ~5.6 million positive and ~758k negative protein-protein interactions (NPPI), that together is ~3.1% what is more, conventional PPI prediction methods produce binary results. At the same time recent studies show that protein binding affinities may prove to be effective in detecting protein complexes, disease association analysis, signaling network reconstruction, etc. In this work we present a fuzzy semantic scoring function using the Gene Ontology (GO) graphs to assess the binding affinity between any two proteins at an organism level. We have implemented a distributed algorithm in Apache Spark that computes this function and processed the complete Human PPI network of ~182 million potential interactions resulting from 19,106 reviewed proteins for which GO annotations are available. The quality of the computed scores has been validated with respect to the available state-of-the-art methods on benchmark data sets.