Relation Extraction of Protein Complexes from Dynamic Protein-Protein Interaction Network

Abstract

Background: Dynamic protein-protein interaction networks (DPPIN) can confirm the conditional and temporal features of proteins and protein complexes. In addition, the relation of protein complexes in dynamic networks can provide useful information in understanding the dynamic functionality of PPI networks.Objective: In this paper, an algorithm is presented to discover the temporal association rule from the dynamic PPIN dataset. Material and Methods:In this analytical study, the static protein-protein interaction network is transformed into a dynamic network using the gene expression thresholding to extract the protein complex relations. The number of presented proteins of the dynamic network is large at each time point. This number will increase for extraction of multidimensional rules at different times. By mapping the gold standard protein complexes as reference protein complexes, the number of items decreases from active proteins to protein complexes at each transaction. Extracted sub graphs as protein complexes, at each time point, are weighted according to the reference protein complexes similarity degrees. Mega-transactions and extended items are created based on occurrence bitmap matrix of the reference complexes. Rules will be extracted based on Mega-transactions of protein complexes. Results:The proposed method has been evaluated using gold standard protein complex rules. The amount of extracted rules from Biogrid datasets and protein complexes are 281, with support 0.2. Conclusion:The characteristic of the proposed algorithm is the simultaneous extraction of intra-transaction and inter-transaction rules. The results evaluation using EBI data shows the efficiency of the proposed algorithm.