Protein function prediction using neighbor relativity in protein-protein interaction network

  • Authors:
  • Sobhan Moosavi;Masoud Rahgozar;Amir Rahimi

  • Affiliations:
  • Database Research Group, Control and Intelligent Processing Center of Excellence, School of Electrical and Computer Engineering, University College of Engineering, University of Tehran, Tehran, Ir ...;Database Research Group, Control and Intelligent Processing Center of Excellence, School of Electrical and Computer Engineering, University College of Engineering, University of Tehran, Tehran, Ir ...;Medicinal and Natural Products Chemistry Research Center, Shiraz University of Medical Science, P.O. Box 71345-3388, Shiraz, Iran and Department of Bioinformatics, Institute of Biochemistry and Bi ...

  • Venue:
  • Computational Biology and Chemistry
  • Year:
  • 2013

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Abstract

There is a large gap between the number of discovered proteins and the number of functionally annotated ones. Due to the high cost of determining protein function by wet-lab research, function prediction has become a major task for computational biology and bioinformatics. Some researches utilize the proteins interaction information to predict function for un-annotated proteins. In this paper, we propose a novel approach called ''Neighbor Relativity Coefficient'' (NRC) based on interaction network topology which estimates the functional similarity between two proteins. NRC is calculated for each pair of proteins based on their graph-based features including distance, common neighbors and the number of paths between them. In order to ascribe function to an un-annotated protein, NRC estimates a weight for each neighbor to transfer its annotation to the unknown protein. Finally, the unknown protein will be annotated by the top score transferred functions. We also investigate the effect of using different coefficients for various types of functions. The proposed method has been evaluated on Saccharomyces cerevisiae and Homo sapiens interaction networks. The performance analysis demonstrates that NRC yields better results in comparison with previous protein function prediction approaches that utilize interaction network.