Improving network topology-based protein interactome mapping via collaborative filtering

Abstract

High-throughput screening (HTS) techniques enable massive identification of protein–protein interactions (PPIs). Nonetheless, it is still intractable to observe the full mapping of PPIs. With acquired PPI data, scalable and inexpensive computation-based approaches to protein interactome mapping (PIM), which aims at increasing the data confidence and predicting new PPIs, are desired in such context. Network topology-based approaches prove to be highly efficient in addressing this issue; yet their performance deteriorates significantly on sparse HTS-PPI networks. This work aims at implementing a highly efficient network topology-based approach to PIM via collaborative filtering (CF), which is a successful approach to addressing sparse matrices for personalized-recommendation. The motivation is that the problems of PIM and personalized-recommendation have similar solution spaces, where the key is to model the relationship among involved entities based on incomplete information. Therefore, it is expected to improve the performance of a topology-based approach on sparse HTS-PPI networks via integrating the idea of CF into it. We firstly model the HTS-PPI data into an incomplete matrix, where each entry describes the interactome weight between corresponding protein pair. Based on it, we transform the functional similarity weight in topology-based approaches into the inter-neighborhood similarity (I-Sim) to model the protein–protein relationship. Finally, we apply saturation-based strategies to the I-Sim model to achieve the CF-enhanced topology-based (CFT) approach to PIM.