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Genome-wide Protein-protein Interaction Screening by Protein-fragment Complementation Assay PCA in Living Cells
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RocSampler: regularizing overlapping protein complexes in protein-protein interaction networks.

Osamu Maruyama1, Yuki Kuwahara2

  • 1Institute of Mathematics for Industry, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan. om@imi.kyushu-u.ac.jp.

BMC Bioinformatics
|December 16, 2017
PubMed
Summary
This summary is machine-generated.

RocSampler effectively predicts protein complexes from protein-protein interaction (PPI) networks, even small ones. This new method improves accuracy by regularizing overlapping complexes and their size distribution.

Keywords:
Markov chain Monte CarloProtein complexProtein-protein interactionRegularization termRocSampler

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Systems Biology

Background:

  • Protein-protein interaction (PPI) networks are crucial for understanding biological processes.
  • Predicting protein complexes from PPI networks is challenging, especially for small complexes and overlapping complexes.
  • Existing databases like CYC2008 contain many small and overlapping protein complexes.

Purpose of the Study:

  • To develop a novel method for predicting protein complexes from PPI networks.
  • To address the difficulties of identifying small protein complexes and modeling overlaps between predicted complexes.

Main Methods:

  • Proposed RocSampler, a sampling-based protein complex prediction method.
  • Incorporated regularization terms for predicted complex overlaps and size distribution into the scoring function.
  • Implemented RocSampler in MATLAB with an executable file available for Windows.

Main Results:

  • RocSampler was applied to five yeast PPI networks.
  • The method demonstrated superior performance compared to existing protein complex prediction methods.
  • The study highlights the effectiveness of regularization terms in scoring functions for protein complex prediction.

Conclusions:

  • The proposed RocSampler method is effective for protein complex prediction.
  • Regularization terms in scoring functions are a promising approach for improving protein complex prediction accuracy.
  • RocSampler offers a valuable tool for analyzing PPI networks and identifying protein complexes.