Title:Prediction of Nitration Sites Based on FCBF Method and Stacking Ensemble Model
Volume: 18
Issue: 5
Author(s): Min Liu, Lu Zhang, Xinyi Qin, Tao Huang, Ziwei Xu and Guangzhong Liu*
Affiliation:
- College of Information Engineering, Shanghai Maritime University, Shanghai,China
Keywords:
PTM (post-translational modification), nitration site, FCBF (fast correlation-based filter), stacking model, overand
under- sampling, Incremental Feature Selection (IFS).
Abstract:
Background: Nitration is an important Post-Translational Modification (PTM) occurring
on the tyrosine residues of proteins. The occurrence of protein tyrosine nitration under disease
conditions is inevitable and represents a shift from the signal transducing physiological actions of -
NO to oxidative and potentially pathogenic pathways. Abnormal protein nitration modification can
lead to serious human diseases, including neurodegenerative diseases, acute respiratory distress, organ
transplant rejection and lung cancer.
Objective: It is necessary and important to identify the nitration sites in protein sequences. Predicting
which tyrosine residues in the protein sequence are nitrated and which are not is of great significance
for the study of nitration mechanism and related diseases.
Methods: In this study, a prediction model of nitration sites based on the over-under sampling strategy
and the FCBF method was proposed by stacking ensemble learning and fusing multiple features.
Firstly, the protein sequence sample was encoded by 2701-dimensional fusion features
(PseAAC, PSSM, AAIndex, CKSAAP, Disorder). Secondly, the ranked feature set was generated
by the FCBF method according to the symmetric uncertainty metric. Thirdly, in the process of model
training, the over- and under- sampling technique was used to tackle the imbalanced dataset. Finally,
the Incremental Feature Selection (IFS) method was adopted to extract an optimal classifier
based on 10-fold cross-validation.
Results and Conclusion: Results show that the model has significant performance advantages in indicators
such as MCC, Recall and F1-score, no matter in what way the comparison was conducted
with other classifiers on the independent test set, or made by cross-validation with single-type feature
or with fusion-features on the training set. By integrating the FCBF feature ranking methods,
over- and under- sampling technique and a stacking model composed of multiple base classifiers,
an effective prediction model for nitration PTM sites was built, which can achieve a better recall
rate when the ratio of positive and negative samples is highly imbalanced.
