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Identification of self-interacting proteins by exploring evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix
An, JY (An, Ji-Yong); You, ZH (You, Zhu-Hong); Chen, X (Chen, Xing); Huang, DS (Huang, De-Shuang); Li, ZW (Li, Zheng-Wei); Liu, G (Liu, Gang); Wang, Y (Wang, Yin); You, ZH
2016
发表期刊ONCOTARGET
卷号7期号:50页码:82440-82449
摘要Self-interacting Proteins (SIPs) play an essential role in a wide range of biological processes, such as gene expression regulation, signal transduction, enzyme activation and immune response. Because of the limitations for experimental self-interaction proteins identification, developing an effective computational method based on protein sequence to detect SIPs is much important. In the study, we proposed a novel computational approach called RVMBIGP that combines the Relevance Vector Machine (RVM) model and Bi-gram probability (BIGP) to predict SIPs based on protein sequence. The proposed prediction model includes as following steps: (1) an effective feature extraction method named BIGP is used to represent protein sequences on Position Specific Scoring Matrix (PSSM); (2) Principal Component Analysis (PCA) method is employed for integrating the useful information and reducing the influence of noise; (3) the robust classifier Relevance Vector Machine (RVM) is used to carry out classification. When performed on yeast and human datasets, the proposed RVMBIGP model can achieve very high accuracies of 95.48% and 98.80%, respectively. The experimental results show that our proposed method is very promising and may provide a cost-effective alternative for SIPs identification. In addition, to facilitate extensive studies for future proteomics research, the RVMBIGP server is freely available for academic use at http://219.219.62.123:8888/RVMBIGP.
关键词Disease Position-specific Scoring Matrix Protein Self-interaction Cancer
DOI10.18632/oncotarget.12517
收录类别SCI
WOS记录号WOS:000391352800040
引用统计
被引频次:3[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.xjipc.cas.cn/handle/365002/4714
专题多语种信息技术研究室
通讯作者You, ZH
作者单位1.China Univ Min & Technol, Sch Comp Sci & Technol, Xuzhou 21116, Peoples R China
2.Chinese Acad Sci, Xinjiang Tech Inst Phys & Chem, Urumqi 830011, Peoples R China
3.China Univ Min & Technol, Sch Informat & Elect Engn, Xuzhou 221116, Peoples R China
4.Tongji Univ, Sch Elect & Informat Engn, Shanghai 201804, Peoples R China
5.Shenzhen Univ, Coll Comp Sci & Software Engn, Shenzhen 518060, Guangdong, Peoples R China
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GB/T 7714
An, JY ,You, ZH ,Chen, X ,et al. Identification of self-interacting proteins by exploring evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix[J]. ONCOTARGET,2016,7(50):82440-82449.
APA An, JY .,You, ZH .,Chen, X .,Huang, DS .,Li, ZW .,...&You, ZH.(2016).Identification of self-interacting proteins by exploring evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix.ONCOTARGET,7(50),82440-82449.
MLA An, JY ,et al."Identification of self-interacting proteins by exploring evolutionary information embedded in PSI-BLAST-constructed position specific scoring matrix".ONCOTARGET 7.50(2016):82440-82449.
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