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  • Title: Motif discovery in biological network using expansion tree.
    Author: Patra S, Mohapatra A.
    Journal: J Bioinform Comput Biol; 2018 Dec; 16(6):1850024. PubMed ID: 30415600.
    Abstract:
    Networks are powerful representation of topological features in biological systems like protein interaction and gene regulation. In order to understand the design principles of such complex networks, the concept of network motifs emerged. Network motifs are recurrent patterns with statistical significance that can be seen as basic building blocks of complex networks. Identification of network motifs leads to many important applications, such as understanding the modularity and the large-scale structure of biological networks, classification of networks into super-families, protein function annotation, etc. However, identification of network motifs is challenging as it involves graph isomorphism which is computationally hard. Though this problem has been studied extensively in the literature using different computational approaches, we are far from satisfactory results. Motivated by the challenges involved in this field, an efficient and scalable network Motif Discovery algorithm based on Expansion Tree (MODET) is proposed. Pattern growth approach is used in this proposed motif-centric algorithm. Each node of the expansion tree represents a non-isomorphic pattern. The embeddings corresponding to a child node of the expansion tree are obtained from the embeddings of the parent node through vertex addition and edge addition. Further, the proposed algorithm does not involve any graph isomorphism check and the time complexities of these processes are O(n) and O(1) , respectively. The proposed algorithm has been tested on Protein-Protein Interaction (PPI) network obtained from the MINT database. The computational efficiency of the proposed algorithm outperforms most of the existing network motif discovery algorithms.
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