A metabolic pathway is a series of biological processes providing necessary molecules and energies for an organism, which could be essential to the lives of the living organisms. Most metabolic pathways require the involvement of compounds and given a compound it is helpful to know what types of metabolic pathways the compound participates in. In this study, compounds are first represented by molecular fragments which are then delivered to a prediction engine called Sequential Minimal Optimization (SMO) for predictions. Maximum relevance and minimum redundancy (mRMR) and incremental feature selection are adopted to extract key features based on which an optimal prediction engine is established. The proposed method is effective comparing to the random forest, Dagging and a popular method that integrating chemical-chemical interactions and chemical-chemical similarities. We also make predictions using some compounds with unknown metabolic pathways and choose 17 compounds for analysis. The results indicate that the method proposed may become a useful tool in predicting and analyzing metabolic pathways.
机构:
Shanghai Univ, Coll Life Sci, Shanghai 200444, Peoples R China
Shanghai Maritime Univ, Coll Informat Engn, Shanghai 201306, Peoples R ChinaShanghai Univ, Coll Life Sci, Shanghai 200444, Peoples R China
Chen, Lei
;
Chu, Chen
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Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Biochem & Cell Biol, Shanghai 200031, Peoples R ChinaShanghai Univ, Coll Life Sci, Shanghai 200444, Peoples R China
Chu, Chen
;
Huang, Tao
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机构:
Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Hlth Sci, Shanghai 200031, Peoples R ChinaShanghai Univ, Coll Life Sci, Shanghai 200444, Peoples R China
Huang, Tao
;
Kong, Xiangyin
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机构:
Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Hlth Sci, Shanghai 200031, Peoples R ChinaShanghai Univ, Coll Life Sci, Shanghai 200444, Peoples R China
Kong, Xiangyin
;
Cai, Yu-Dong
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机构:
Shanghai Univ, Coll Life Sci, Shanghai 200444, Peoples R ChinaShanghai Univ, Coll Life Sci, Shanghai 200444, Peoples R China
机构:
Shanghai Maritime Univ, Coll Informat Engn, Shanghai, Peoples R ChinaShanghai Maritime Univ, Coll Informat Engn, Shanghai, Peoples R China
Chen, Lei
;
Zeng, Wei-Ming
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机构:
Shanghai Maritime Univ, Coll Informat Engn, Shanghai, Peoples R ChinaShanghai Maritime Univ, Coll Informat Engn, Shanghai, Peoples R China
Zeng, Wei-Ming
;
Cai, Yu-Dong
论文数: 0引用数: 0
h-index: 0
机构:
Shanghai Univ, Inst Syst Biol, Shanghai, Peoples R China
Gordon Life Sci Inst, San Diego, CA USAShanghai Maritime Univ, Coll Informat Engn, Shanghai, Peoples R China
Cai, Yu-Dong
;
Feng, Kai-Yan
论文数: 0引用数: 0
h-index: 0
机构:
Shanghai Ctr Bioinformat Technol, Shanghai, Peoples R China
Chinese Acad Sci, Shanghai Inst Biol Sci, Key Lab Syst Biol, Shanghai, Peoples R ChinaShanghai Maritime Univ, Coll Informat Engn, Shanghai, Peoples R China
Feng, Kai-Yan
;
Chou, Kuo-Chen
论文数: 0引用数: 0
h-index: 0
机构:
Gordon Life Sci Inst, San Diego, CA USAShanghai Maritime Univ, Coll Informat Engn, Shanghai, Peoples R China
机构:
Fudan Univ, Ctr Computat Syst Biol, Shanghai 200433, Peoples R China
E China Normal Univ, Shanghai Key Lab Trustworthy Comp, Shanghai 200062, Peoples R ChinaShanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China
Chen, Lei
;
Shi, Xiaohe
论文数: 0引用数: 0
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机构:
Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Hlth Sci, Shanghai 200025, Peoples R China
Shanghai Jiao Tong Univ, Sch Med, Shanghai 200025, Peoples R ChinaShanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China
Shi, Xiaohe
;
Kong, Xiangyin
论文数: 0引用数: 0
h-index: 0
机构:
Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Hlth Sci, Shanghai 200025, Peoples R China
Shanghai Jiao Tong Univ, Sch Med, Shanghai 200025, Peoples R ChinaShanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China
Kong, Xiangyin
;
Zeng, Zhenbing
论文数: 0引用数: 0
h-index: 0
机构:
E China Normal Univ, Shanghai Key Lab Trustworthy Comp, Shanghai 200062, Peoples R ChinaShanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China
Zeng, Zhenbing
;
Cai, Yu-Dong
论文数: 0引用数: 0
h-index: 0
机构:
Shanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R ChinaShanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China
机构:
Shanghai Univ, Coll Life Sci, Shanghai 200444, Peoples R China
Shanghai Maritime Univ, Coll Informat Engn, Shanghai 201306, Peoples R ChinaShanghai Univ, Coll Life Sci, Shanghai 200444, Peoples R China
Chen, Lei
;
Chu, Chen
论文数: 0引用数: 0
h-index: 0
机构:
Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Biochem & Cell Biol, Shanghai 200031, Peoples R ChinaShanghai Univ, Coll Life Sci, Shanghai 200444, Peoples R China
Chu, Chen
;
Huang, Tao
论文数: 0引用数: 0
h-index: 0
机构:
Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Hlth Sci, Shanghai 200031, Peoples R ChinaShanghai Univ, Coll Life Sci, Shanghai 200444, Peoples R China
Huang, Tao
;
Kong, Xiangyin
论文数: 0引用数: 0
h-index: 0
机构:
Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Hlth Sci, Shanghai 200031, Peoples R ChinaShanghai Univ, Coll Life Sci, Shanghai 200444, Peoples R China
Kong, Xiangyin
;
Cai, Yu-Dong
论文数: 0引用数: 0
h-index: 0
机构:
Shanghai Univ, Coll Life Sci, Shanghai 200444, Peoples R ChinaShanghai Univ, Coll Life Sci, Shanghai 200444, Peoples R China
机构:
Shanghai Maritime Univ, Coll Informat Engn, Shanghai, Peoples R ChinaShanghai Maritime Univ, Coll Informat Engn, Shanghai, Peoples R China
Chen, Lei
;
Zeng, Wei-Ming
论文数: 0引用数: 0
h-index: 0
机构:
Shanghai Maritime Univ, Coll Informat Engn, Shanghai, Peoples R ChinaShanghai Maritime Univ, Coll Informat Engn, Shanghai, Peoples R China
Zeng, Wei-Ming
;
Cai, Yu-Dong
论文数: 0引用数: 0
h-index: 0
机构:
Shanghai Univ, Inst Syst Biol, Shanghai, Peoples R China
Gordon Life Sci Inst, San Diego, CA USAShanghai Maritime Univ, Coll Informat Engn, Shanghai, Peoples R China
Cai, Yu-Dong
;
Feng, Kai-Yan
论文数: 0引用数: 0
h-index: 0
机构:
Shanghai Ctr Bioinformat Technol, Shanghai, Peoples R China
Chinese Acad Sci, Shanghai Inst Biol Sci, Key Lab Syst Biol, Shanghai, Peoples R ChinaShanghai Maritime Univ, Coll Informat Engn, Shanghai, Peoples R China
Feng, Kai-Yan
;
Chou, Kuo-Chen
论文数: 0引用数: 0
h-index: 0
机构:
Gordon Life Sci Inst, San Diego, CA USAShanghai Maritime Univ, Coll Informat Engn, Shanghai, Peoples R China
机构:
Fudan Univ, Ctr Computat Syst Biol, Shanghai 200433, Peoples R China
E China Normal Univ, Shanghai Key Lab Trustworthy Comp, Shanghai 200062, Peoples R ChinaShanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China
Chen, Lei
;
Shi, Xiaohe
论文数: 0引用数: 0
h-index: 0
机构:
Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Hlth Sci, Shanghai 200025, Peoples R China
Shanghai Jiao Tong Univ, Sch Med, Shanghai 200025, Peoples R ChinaShanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China
Shi, Xiaohe
;
Kong, Xiangyin
论文数: 0引用数: 0
h-index: 0
机构:
Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Hlth Sci, Shanghai 200025, Peoples R China
Shanghai Jiao Tong Univ, Sch Med, Shanghai 200025, Peoples R ChinaShanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China
Kong, Xiangyin
;
Zeng, Zhenbing
论文数: 0引用数: 0
h-index: 0
机构:
E China Normal Univ, Shanghai Key Lab Trustworthy Comp, Shanghai 200062, Peoples R ChinaShanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China
Zeng, Zhenbing
;
Cai, Yu-Dong
论文数: 0引用数: 0
h-index: 0
机构:
Shanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R ChinaShanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China