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EURASIP Journal on Advances in Signal Processing
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Towards Inferring Protein Interactions: Challenges and Solutions

EURASIP Journal on Advances in Signal Processing volume 2006, Article number: 037349 (2006) Cite this article

Abstract

Discovering interacting proteins has been an essential part of functional genomics. However, existing experimental techniques only uncover a small portion of any interactome. Furthermore, these data often have a very high false rate. By conceptualizing the interactions at domain level, we provide a more abstract representation of interactome, which also facilitates the discovery of unobserved protein-protein interactions. Although several domain-based approaches have been proposed to predict protein-protein interactions, they usually assume that domain interactions are independent on each other for the convenience of computational modeling. A new framework to predict protein interactions is proposed in this paper, where no assumption is made about domain interactions. Protein interactions may be the result of multiple domain interactions which are dependent on each other. A conjunctive norm form representation is used to capture the relationships between protein interactions and domain interactions. The problem of interaction inference is then modeled as a constraint satisfiability problem and solved via linear programing. Experimental results on a combined yeast data set have demonstrated the robustness and the accuracy of the proposed algorithm. Moreover, we also map some predicted interacting domains to three-dimensional structures of protein complexes to show the validity of our predictions.

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Authors and Affiliations

  1. Information and Telecommunication Technology Center, The University of Kansas, Lawrence, KS, 66045, USA

    Ya Zhang

  2. Department of Electrical Engineering and Computer Science, The University of Kansas, Lawrence, KS, 66045, USA

    Ya Zhang

  3. Department of Computer Science and Engineering, School of Engineering, Pennsylvania State University, University Park, PA, 16802, USA

    Hongyuan Zha

  4. College of Information Sciences and Technology, Pennsylvania State University, University Park, PA, 16802-6823, USA

    Chao-Hsien Chu

  5. NEC Laboratories America, Inc., Cupertino, CA, 95014, USA

    Xiang Ji

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  1. Ya Zhang
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  2. Hongyuan Zha
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  3. Chao-Hsien Chu
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  4. Xiang Ji
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Correspondence to Ya Zhang.

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Open Access This article is distributed under the terms of the Creative Commons Attribution 2.0 International License ( https://creativecommons.org/licenses/by/2.0 ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Zhang, Y., Zha, H., Chu, CH. et al. Towards Inferring Protein Interactions: Challenges and Solutions. EURASIP J. Adv. Signal Process. 2006, 037349 (2006). https://doi.org/10.1155/ASP/2006/37349

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