Prediction of subcellular location apoptosis proteins with ensemble classifier and feature selection.
Apoptosis proteins have a central role in the development and the homeostasis of an organism. These proteins are very important for understanding the mechanism of programmed cell death. The function of an apoptosis protein is closely related to its subcellular location. It is crucial to develop powerful tools to predict apoptosis protein locations for rapidly increasing gap between the number of known structural proteins and the number of known sequences in protein databank. In this study, amino acids pair compositions with different spaces are used to construct feature sets for representing sample of protein feature selection approach based on binary particle swarm optimization, which is applied to extract effective feature. Ensemble classifier is used as prediction engine, of which the basic classifier is the fuzzy K-nearest neighbor. Each basic classifier is trained with different feature sets. Two datasets often used in prior works are selected to validate the performance of proposed approach. The results obtained by jackknife test are quite encouraging, indicating that the proposed method might become a potentially useful tool for subcellular location of apoptosis protein, or at least can play a complimentary role to the existing methods in the relevant areas. The supplement information and software written in Matlab are available by contacting the corresponding author.
Gu
Quan
Q
College of Information Sciences and Technology, Donghua University, 201620, Shanghai, China.
Ding
Yong-Sheng
YS
Jiang
Xiao-Ying
XY
Zhang
Tong-Liang
TL
D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D051017:Apoptosis Regulatory Proteins / Q000737:chemistry* / Q000145:classification / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D005103:Expert Systems; D017143:Fuzzy Logic; D006801:Humans; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D013347:Subcellular Fractions / Q000378:metabolism
D051017:Apoptosis Regulatory Proteins