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Identifying Essential Proteins by Purifying Protein Interaction Networks

  • Min LiEmail author
  • Xiaopei Chen
  • Peng Ni
  • Jianxin Wang
  • Yi PanEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 9683)

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.

Keywords

Positive Predictive Value Negative Predictive Value Degree Centrality Betweenness Centrality Protein Interaction Network 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer International Publishing Switzerland 2016

Authors and Affiliations

  1. 1.School of Information Science and EngineeringCentral South UniversityChangshaChina
  2. 2.Department of Computer ScienceGeorgia State UniversityAtlantaUSA

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