Prediction of tyrosine sulfation with mRMR feature selection and analysis.
Protein tyrosine sulfation is a ubiquitous post-translational modification (PTM) of secreted and transmembrane proteins that pass through the Golgi apparatus. In this study, we developed a new method for protein tyrosine sulfation prediction based on a nearest neighbor algorithm with the maximum relevance minimum redundancy (mRMR) method followed by incremental feature selection (IFS). We incorporated features of sequence conservation, residual disorder, and amino acid factor, 229 features in total, to predict tyrosine sulfation sites. From these 229 features, 145 features were selected and deemed as the optimized features for the prediction. The prediction model achieved a prediction accuracy of 90.01% using the optimal 145-feature set. Feature analysis showed that conservation, disorder, and physicochemical/biochemical properties of amino acids all contributed to the sulfation process. Site-specific feature analysis showed that the features derived from its surrounding sites contributed profoundly to sulfation site determination in addition to features derived from the sulfation site itself. The detailed feature analysis in this paper might help understand more of the sulfation mechanism and guide the related experimental validation.
Niu
Shen
S
Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, PR China.
Huang
Tao
T
Feng
Kaiyan
K
Cai
Yudong
Y
Li
Yixue
Y
D000465:Algorithms; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D011506:Proteins / Q000378:metabolism*; D015203:Reproducibility of Results; D012984:Software; D013431:Sulfates / Q000378:metabolism; D014443:Tyrosine / Q000378:metabolism*
D011506:Proteins; D013431:Sulfates; D014443:Tyrosine