A new method for predicting essential proteins based on participation degree in protein complex and subgraph density

PLoS One. 2018 Jun 12;13(6):e0198998. doi: 10.1371/journal.pone.0198998. eCollection 2018.

Abstract

Essential proteins are crucial to living cells. Identification of essential proteins from protein-protein interaction (PPI) networks can be applied to pathway analysis and function prediction, furthermore, it can contribute to disease diagnosis and drug design. There have been some experimental and computational methods designed to identify essential proteins, however, the prediction precision remains to be improved. In this paper, we propose a new method for identifying essential proteins based on Participation degree of a protein in protein Complexes and Subgraph Density, named as PCSD. In order to test the performance of PCSD, four PPI datasets (DIP, Krogan, MIPS and Gavin) are used to conduct experiments. The experiment results have demonstrated that PCSD achieves a better performance for predicting essential proteins compared with some competing methods including DC, SC, EC, IC, LAC, NC, WDC, PeC, UDoNC, and compared with the most recent method LBCC, PCSD can correctly predict more essential proteins from certain numbers of top ranked proteins on the DIP dataset, which indicates that PCSD is very effective in discovering essential proteins in most case.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Computational Biology / methods*
  • Genes, Essential*
  • Protein Interaction Mapping / methods*
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism*

Substances

  • Saccharomyces cerevisiae Proteins

Grants and funding

This paper is supported by the National Natural Science Foundation of China (61672334, 61502290, 61401263). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.