PUP-Fuse: Prediction of Protein Pupylation Sites by Integrating Multiple Sequence Representations
Abstract
:1. Introduction
2. Results and Discussion
2.1. Sequence Preference Analysis
2.2. Performance Results on Training Dataset
2.3. Performance Optimization by Chi-Square Test
2.4. Comparison among Different ML Methods on Training Dataset
2.5. Comparison of PUP-Fuse with Existing Methods on Independent Dataset
3. Materials and Methods
3.1. Data Collection and Processing
3.2. Encoding Scheme
3.2.1. pbCKSAAP
3.2.2. CKSAAP Encoding
3.2.3. Binary Encoding
3.2.4. TPC Encoding
3.2.5. AAI Encoding
3.2.6. Feature Selection
3.2.7. Classification Method
3.2.8. Feature Integration
3.2.9. Model Evaluation
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Encoding Method | Sens | Spec | Acc | MCC | AUC | p-Value |
---|---|---|---|---|---|---|
AAI | 0.482 | 0.811 | 0.651 | 0.313 | 0.697 | <0.01 |
Binary | 0.510 | 0.810 | 0.661 | 0.331 | 0.703 | <0.01 |
pbCKSAAP | 0.782 | 0.800 | 0.800 | 0.590 | 0.908 | 0.034 |
TPC | 0.770 | 0.801 | 0.791 | 0.574 | 0.877 | 0.021 |
CKSAAP | 0.773 | 0.805 | 0.789 | 0.583 | 0.895 | 0.038 |
PUP-Fuse | 0.802 | 0.820 | 0.811 | 0.623 | 0.912 |
Encoding Method | Sens | Spec | Acc | MCC | AUC | p-Value |
---|---|---|---|---|---|---|
AAI | 0.410 | 0.854 | 0.626 | 0.294 | 0.724 | <0.01 |
Binary | 0.417 | 0.855 | 0.629 | 0.305 | 0.731 | <0.01 |
pbCKSAAP | 0.831 | 0.827 | 0.829 | 0.658 | 0.929 | 0.031 |
TPC | 0.754 | 0.827 | 0.789 | 0.582 | 0.878 | <0.01 |
CKSAAP | 0.822 | 0.825 | 0.824 | 0.646 | 0.911 | <0.026 |
PUP-Fuse | 0.886 | 0.881 | 0.884 | 0.768 | 0.956 |
Methods | Sens | Spec | Acc | MCC |
---|---|---|---|---|
iPUP | 0.40 | 0.88 | 0.73 | 0.32 |
GPS-PUP | 0.21 | 0.89 | 0.68 | 0.13 |
PUPS | 0.17 | 0.89 | 0.67 | 0.08 |
pbPUP | 0.48 | 0.82 | 0.79 | 0.45 |
PUP-Fuse | 0.59 | 0.91 | 0.82 | 0.55 |
Training | Independent | |
---|---|---|
Pupylated protein | 162 | 71 |
Pupylated lysine | 186 | 87 |
Non-pupylated lysine | 186 | 191 |
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Auliah, F.N.; Nilamyani, A.N.; Shoombuatong, W.; Alam, M.A.; Hasan, M.M.; Kurata, H. PUP-Fuse: Prediction of Protein Pupylation Sites by Integrating Multiple Sequence Representations. Int. J. Mol. Sci. 2021, 22, 2120. https://doi.org/10.3390/ijms22042120
Auliah FN, Nilamyani AN, Shoombuatong W, Alam MA, Hasan MM, Kurata H. PUP-Fuse: Prediction of Protein Pupylation Sites by Integrating Multiple Sequence Representations. International Journal of Molecular Sciences. 2021; 22(4):2120. https://doi.org/10.3390/ijms22042120
Chicago/Turabian StyleAuliah, Firda Nurul, Andi Nur Nilamyani, Watshara Shoombuatong, Md Ashad Alam, Md Mehedi Hasan, and Hiroyuki Kurata. 2021. "PUP-Fuse: Prediction of Protein Pupylation Sites by Integrating Multiple Sequence Representations" International Journal of Molecular Sciences 22, no. 4: 2120. https://doi.org/10.3390/ijms22042120
APA StyleAuliah, F. N., Nilamyani, A. N., Shoombuatong, W., Alam, M. A., Hasan, M. M., & Kurata, H. (2021). PUP-Fuse: Prediction of Protein Pupylation Sites by Integrating Multiple Sequence Representations. International Journal of Molecular Sciences, 22(4), 2120. https://doi.org/10.3390/ijms22042120