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Identifying Essential Proteins by Purifying Protein Interaction Networks

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Bioinformatics Research and Applications (ISBRA 2016)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 9683))

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Abstract

Identification of essential proteins based on protein interaction network (PIN) is a very important and hot topic in the post genome era. In this paper, we propose a new method to identify essential proteins based on the purified PIN by using gene expression profiles and subcellular location information. The basic idea behind the proposed purifying method is that two proteins can physically interact with each other only if they appear together at the same subcellular location and are active together at least at a time point in the cell cycle. The original static PIN is marked as S-PIN and the final PIN purified by our method is marked as TS-PIN. To evaluate whether the constructed TS-PIN is more suitable to being used in the identification of essential proteins, six network-based essential protein discovery methods (DC, EC, SC, BC, CC, and IC) are applied on it to identify essential proteins. It is the same way with S-PIN and NF-APIN. NF-APIN is a dynamic PIN constructed by using gene expression data and S-PIN. The experimental results on the protein interaction network of S.cerevisiae shows that all the six network-based methods achieve better results when being applied on TS-PIN than that being applied on S-PIN and NF-APIN.

Y Pan—This work was supported in part by the National Natural Science Foundation of China under Grants (No.61370024, No.61232001, and No.61428209) and the Program for New Century Excellent Talents in University(NCET-12-0547).

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Authors and Affiliations

  1. School of Information Science and Engineering, Central South University, Changsha, 410083, China

    Min Li, Xiaopei Chen, Peng Ni, Jianxin Wang & Yi Pan

  2. Department of Computer Science, Georgia State University, Atlanta, GA, 30302-4110, USA

    Yi Pan

Authors
  1. Min Li
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  2. Xiaopei Chen
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  3. Peng Ni
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  4. Jianxin Wang
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  5. Yi Pan
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Corresponding authors

Correspondence to Min Li or Yi Pan .

Editor information

Editors and Affiliations

  1. Dept. of Computer Science, Georgia State University, Atlanta, Georgia, USA

    Anu Bourgeois

  2. Centre for Disease Control & Prevention, Atlanta, Georgia, USA

    Pavel Skums

  3. Department of Computer Science, Hong Kong Baptist University, Kowloon Tong, Hong Kong

    Xiang Wan

  4. Georgia State University, Atlanta, Georgia, USA

    Alex Zelikovsky

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© 2016 Springer International Publishing Switzerland

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Li, M., Chen, X., Ni, P., Wang, J., Pan, Y. (2016). Identifying Essential Proteins by Purifying Protein Interaction Networks. In: Bourgeois, A., Skums, P., Wan, X., Zelikovsky, A. (eds) Bioinformatics Research and Applications. ISBRA 2016. Lecture Notes in Computer Science(), vol 9683. Springer, Cham. https://doi.org/10.1007/978-3-319-38782-6_9

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  • DOI: https://doi.org/10.1007/978-3-319-38782-6_9

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-38781-9

  • Online ISBN: 978-3-319-38782-6

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