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Detection of Protein-Protein Interactions from Amino Acid Sequences Using a Rotation Forest Model with a Novel PR-LPQ Descriptor

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Advanced Intelligent Computing Theories and Applications (ICIC 2015)

Part of the book series: Lecture Notes in Computer Science ((LNAI,volume 9227))

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Abstract

Protein-protein interactions (PPIs) play an essential role in almost all cellular processes. In this article, a sequence-based method is proposed to detect PPIs by combining Rotation Forest (RF) model with a novel feature representation. In the procedure of the feature representation, we first adopt the Physicochemical Property Response Matrix (PR) method to transform the amino acids sequence into a matrix and then employ the Local Phase Quantization (LPQ)-based texture descriptor to extract the local phrase information in the matrix. When performed on the PPIs dataset of Saccharomyces cerevisiae, the proposed method achieves the high prediction accuracy of 93.92 % with 91.10 % sensitivity at 96.45 % precision. Compared with the existing sequence-based method, the results of the proposed method demonstrate that it is a meaningful tool for future proteomics research.

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Acknowledgments

This work is supported in part by the National Science Foundation of China, under Grants 61373086, 61202347, and 61401385, in part by the Guangdong Natural Science Foundation under Grant 2014A030313555, and in part by the Shenzhen Scientific Research and Development Funding Program under grants JCYJ20140418095735569.

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Authors and Affiliations

  1. College of Computer Science and Software Engineering, Shenzhen University, Shenzhen, 518060, Guangdong, China

    Leon Wong, Zhu-Hong You, Shuai Li, Yu-An Huang & Gang Liu

Authors
  1. Leon Wong
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  2. Zhu-Hong You
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  3. Shuai Li
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  4. Yu-An Huang
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  5. Gang Liu
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Corresponding author

Correspondence to Leon Wong .

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Editors and Affiliations

  1. Tongji University, Shanghai, China

    De-Shuang Huang

  2. Incheon, Korea (Republic of)

    Kyungsook Han

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Wong, L., You, ZH., Li, S., Huang, YA., Liu, G. (2015). Detection of Protein-Protein Interactions from Amino Acid Sequences Using a Rotation Forest Model with a Novel PR-LPQ Descriptor. In: Huang, DS., Han, K. (eds) Advanced Intelligent Computing Theories and Applications. ICIC 2015. Lecture Notes in Computer Science(), vol 9227. Springer, Cham. https://doi.org/10.1007/978-3-319-22053-6_75

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  • DOI: https://doi.org/10.1007/978-3-319-22053-6_75

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-22052-9

  • Online ISBN: 978-3-319-22053-6

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