ActivePPI: quantifying protein-protein interaction network activity with Markov random fields.

Journal: Bioinformatics (Oxford, England)
Published Date: Sep 2, 2023

Abstract

MOTIVATION: Protein-protein interactions (PPI) are crucial components of the biomolecular networks that enable cells to function. Biological experiments have identified a large number of PPI, and these interactions are stored in knowledge bases. However, these interactions are often restricted to specific cellular environments and conditions. Network activity can be characterized as the extent of agreement between a PPI network (PPIN) and a distinct cellular environment measured by protein mass spectrometry, and it can also be quantified as a statistical significance score. Without knowing the activity of these PPI in the cellular environments or specific phenotypes, it is impossible to reveal how these PPI perform and affect cellular functioning.

Authors

  • Chuanyuan Wang
    Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, Shandong 250061, China.
  • Shiyu Xu
    School of Electrical Engineering, Sichuan University, Chengdu 610065, P. R. China.
  • Duanchen Sun
    Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing, 100190, China.
  • Zhi-ping Liu

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