CombiMotif: A new algorithm for network motifs discovery in protein–protein interaction networks

Jiawei Luo, Guanghui Li, Dan Song and Cheng Liang

Physica A: Statistical Mechanics and its Applications, 2014, vol. 416, issue C, 309-320

Abstract: Discovering motifs in protein–protein interaction networks is becoming a current major challenge in computational biology, since the distribution of the number of network motifs can reveal significant systemic differences among species. However, this task can be computationally expensive because of the involvement of graph isomorphic detection. In this paper, we present a new algorithm (CombiMotif) that incorporates combinatorial techniques to count non-induced occurrences of subgraph topologies in the form of trees. The efficiency of our algorithm is demonstrated by comparing the obtained results with the current state-of-the art subgraph counting algorithms. We also show major differences between unicellular and multicellular organisms. The datasets and source code of CombiMotif are freely available upon request.

Keywords: Protein–protein interaction networks; Network motif; Non-induced subgraphs; Subgraph isomorphism; Combinatorial techniques (search for similar items in EconPapers)
Date: 2014
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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:416:y:2014:i:c:p:309-320

DOI: 10.1016/j.physa.2014.08.062

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