Predicting mirna's target from primary structure by the nearest neighbor algorithm
文献类型：期刊论文
| 作者 | Lin, Kao1; Qian, Ziliang2,3; Lu, Lin; Lu, Lingyi; Lai, Lihui5; Gu, Jieyi5; Zeng, Zhenbing6; Li, Haipeng1; Cai, Yudong7 |
| 刊名 | Molecular diversity
 |
| 出版日期 | 2010-11-01 |
| 卷号 | 14期号:4页码:719-729 |
| 关键词 | Mirna Target Predict Nearest neighbor algorithm Minimum redundancy maximum relevance Properties forward selection |
| ISSN号 | 1381-1991 |
| DOI | 10.1007/s11030-009-9216-y |
| 通讯作者 | Li, haipeng(lihaipeng@picb.ac.cn) |
| 英文摘要 | We used a machine learning method, the nearest neighbor algorithm (nna), to learn the relationship between mirnas and their target proteins, generating a predictor which can then judge whether a new mirna-target pair is true or not. we acquired 198 positive (true) mirna-target pairs from tarbase and the literature, and generated 4,888 negative (false) pairs through random combination. a 0/1 system and the frequencies of single nucleotides and di-nucleotides were used to encode mirnas into vectors while various physicochemical parameters were used to encode the targets. the nna was then applied, learning from these data to produce a predictor. we implemented minimum redundancy maximum relevance (mrmr) and properties forward selection (pfs) to reduce the redundancy of our encoding system, obtaining 91 most efficient properties. finally, via the jackknife cross-validation test, we got a positive accuracy of 69.2% and an overall accuracy of 96.0% with all the 253 properties. besides, we got a positive accuracy of 83.8% and an overall accuracy of 97.2% with the 91 most efficient properties. a web-server for predictions is also made available at http://app3.biosino.org:8080/mirtp/index.jsp. |
| WOS关键词 | PROTEIN-PROTEIN INTERACTIONS ; DNA-BINDING PROTEINS ; MICRORNA TARGETS ; CLASSIFICATION ; SEQUENCE ; INFORMATION ; EXPRESSION ; SIRNAS ; SERVER ; GENES |
| WOS研究方向 | Biochemistry & Molecular Biology ; Chemistry ; Pharmacology & Pharmacy |
| WOS类目 | Biochemistry & Molecular Biology ; Chemistry, Applied ; Chemistry, Medicinal ; Chemistry, Multidisciplinary |
| 语种 | 英语 |
| WOS记录号 | WOS:000284598600012 |
| 出版者 | SPRINGER |
| URI标识 | http://www.irgrid.ac.cn/handle/1471x/2407147 |
| 专题 | 中国科学院大学 |
| 通讯作者 | Li, Haipeng |
| 作者单位 | 1.Chinese Acad Sci, Shanghai Inst Biol Sci, CAS MPG Partner Inst Computat Biol, Shanghai 200031, Peoples R China 2.Chinese Acad Sci, Grad Sch, Beijing 100039, Peoples R China 3.Chinese Acad Sci, Shanghai Inst Biol Sci, Key Lab Mol Syst Biol, Bioinformat Ctr, Shanghai 200031, Peoples R China 4.Shanghai Jiao Tong Univ, Dept Biomed Engn, Shanghai 200040, Peoples R China 5.E China Normal Univ, Sch Life Sci, Shanghai 200062, Peoples R China 6.E China Normal Univ, Inst Software Engn, Shanghai 200062, Peoples R China 7.Shanghai Univ, Inst Syst Biol, Shanghai 200444, Peoples R China |
| 推荐引用方式 GB/T 7714 | Lin, Kao,Qian, Ziliang,Lu, Lin,et al. Predicting mirna's target from primary structure by the nearest neighbor algorithm[J]. Molecular diversity,2010,14(4):719-729. |
| APA | Lin, Kao.,Qian, Ziliang.,Lu, Lin.,Lu, Lingyi.,Lai, Lihui.,...&Cai, Yudong.(2010).Predicting mirna's target from primary structure by the nearest neighbor algorithm.Molecular diversity,14(4),719-729. |
| MLA | Lin, Kao,et al."Predicting mirna's target from primary structure by the nearest neighbor algorithm".Molecular diversity 14.4(2010):719-729. |
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来源：中国科学院大学
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