Discovering driver nodes in chronic kidney disease-related networks using Trader as a newly developed algorithm

Abstract

Thanks to the advances in the field of computational-based biology, a huge volume of disease-related data has been generated so far. From the existing data, the disease-related protein-protein interaction (PPI) networks seem to yield effective treatment plans due to the informative/systematic representation of diseases. Yet, a large number of previous studies have failed due to the complex nature of such disease-related networks. For addressing this limitation, in the present study, we combined Trader and the DFS algorithms to identify a minimal subset of nodes (driver nodes) whose removal produces a maximum number of disjoint sub-networks. We then screened the nodes in the disease-associated PPI networks and to evaluate the efficiency of the suggested method, it was applied to six PPI networks of differentially expressed genes in chronic kidney diseases. The performance of Trader was superior to other well-known algorithms in terms of identifying driver nodes. Besides, the proportion of proteins that were targeted by at least one FDA-approved drug was significantly higher among the identified driver nodes when compared with the rest of the proteins in the networks. The proposed algorithm could be applied for predicting future therapeutic targets in complex disorder networks. In conclusion, unlike the common methods, computationally efficient algorithms can generate more practical outcomes which are compatible with real-world biological facts.