Title: Assessing protein-protein interactions based on the semantic similarity of interacting proteins

Authors: Guangyu Cui; Byungmin Kim; Saud Alguwaizani; Kyungsook Han

Addresses: School of Computer Science and Engineering, Inha University, Incheon 402-751, Korea ' School of Computer Science and Engineering, Inha University, Incheon 402-751, Korea ' School of Computer Science and Engineering, Inha University, Incheon 402-751, Korea ' School of Computer Science and Engineering, Inha University, Incheon 402-751, Korea

Abstract: The Gene Ontology (GO) has been used in estimating the semantic similarity of proteins since it has the largest and reliable vocabulary of gene products and characteristics. We developed a new method which can assess Protein-Protein Interactions (PPI) using the branching factor and information content of the common ancestor of interacting proteins in the GO hierarchy. We performed a comparative evaluation of the measure with other GO-based similarity measures and evaluation results showed that our method outperformed others in most GO domains.

Keywords: semantic similarity; protein-protein interactions; PPI; branching factor; GO terms; gene ontology; interacting proteins; bioinformatics.

DOI: 10.1504/IJDMB.2015.070842

International Journal of Data Mining and Bioinformatics, 2015 Vol.13 No.1, pp.75 - 83

Received: 24 Feb 2014
Accepted: 03 Mar 2014

Published online: 30 Jul 2015 *

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