Predict protein-protein interactions from protein primary sequences: using wavelet transform combined with stacking algorithm
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Abstract
Most biological processes within a cell are carried out by protein-protein interaction (PPI) networks, or so called interactomics. Therefore, identification of PPIs is crucial to elucidating protein functions and further understanding of various cellular biological processes. Currently, a series of high-throughput experimental technologies for detect PPIs have been presented. However, the time-consuming and labor-driven characteristics of these methods forced people to turn to virtual technology for PPIs prediction. Herein, we developed a new predictor which uses stacking algorithm with information extraction by wavelet transform. When applied on the Saccharomyces cerevisiae PPI dataset, the proposed method got a prediction accuracy of 83.35% with sensitivity of 92.95% at the specificity of 65.41%. An independent data set of 2726 Helicobacter pylori PPIs was also used to evaluate this prediction model, and the prediction accuracy is 80.39%, which is better than that of most existing methods.
Cite this as
2017. Predict protein-protein interactions from protein primary sequences: using wavelet transform combined with stacking algorithm. PeerJ Preprints 5:e2964v1 https://doi.org/10.7287/peerj.preprints.2964v1Author comment
This is a submission to PeerJ for review.
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Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Pin-San Xu conceived and designed the experiments, wrote the paper, prepared figures and/or tables.
Jun Luo performed the experiments, analyzed the data, reviewed drafts of the paper.
Tong-Yi Dou contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Data Deposition
The following information was supplied regarding data availability:
(1) GitHub
(2) master_experiment_stacking
Funding
This work was sponsored by the National Natural Science Foundation of China (No. 31600641). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
