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An Improved Method for Identification of Pre-miRNA in < italic > Drosophila

文献类型：期刊论文

作者Yu, Tieying1,3,4; Chen, Min3,4; Wang, Chunde2,3,4
刊名IEEE ACCESS
出版日期2020
卷号8页码:52173-52180
关键词microRNA iLearn PyFeat Pse-in-One MRMD2 0 t-SNE accuracy random forest discriminative features
ISSN号2169-3536
DOI10.1109/ACCESS.2020.2980897
通讯作者Wang, Chunde(chundewang2007@163.com)
英文摘要Identification of microRNAs is important in studies of regulation of gene expression in many biologyical processes. In this study, we developed an improved method for identification of microRNAs in Drosophila. We used the iLearn, PyFeat, and Pse-in-One methods to extract the features and then used Max-Relevance-Max-Distance (MRMD2.0) and t-Distributed Stochastic Neighbour Embedding (t-SNE) to reduce dimension of the features and the random forest classifier in Weka to identify miRNAs. With this method, we found that the discriminative features for identification of pre-miRNAs were, in Drosophila melanogaster, the occurrences of G & x005F;GUG and C & x005F;AGU when the value of the feature vector was greater than 2, and in Drosophila pseudoobscura, the 4-tuple nucleotide composition and the occurrence of 4-length neighbouring nucleic acids when the value of the feature vector was less than 0.02. These vectors covered all compositional information or the frequency of bases. Classification results showed the classification accuracy was 95.7 & x0025; and 93.6 & x0025;, the precision rate was 95.8 & x0025; and 93.6 & x0025;, and the recall rate was 95.7 & x0025; and 93.6 & x0025; in Drosophila melanogaster and Drosophila pseudoobscura, respectively, which are higher than those reported in previous studies.
WOS关键词MICRORNA-DISEASE ASSOCIATIONS ; IDENTIFYING PROMOTERS ; GENE-EXPRESSION ; PREDICTION ; RNA ; SITES ; DNA ; METHYLATION ; DATABASE ; NETWORK
WOS研究方向Computer Science ; Engineering ; Telecommunications
语种英语
WOS记录号WOS:000524748500085
资助机构Natural Science Foundation of China
源URL[http://ir.yic.ac.cn/handle/133337/41410]  
专题海岸带生物学与生物资源利用重点实验室
通讯作者Wang, Chunde
作者单位1.Shandong Agr Univ, Coll Life Sci, Tai An 271018, Shandong, Peoples R China
2.Qingdao Agr Univ, Marine Sci & Engn Coll, Qingdao 266109, Peoples R China
3.Chinese Acad Sci, Yantai Inst Coastal Zone Res, Yantai 264003, Peoples R China
4.Chinese Acad Sci, Ctr Ocean Mega Sci, Yantai 264003, Peoples R China
推荐引用方式
GB/T 7714		 Yu, Tieying,Chen, Min,Wang, Chunde. An Improved Method for Identification of Pre-miRNA in < italic > Drosophila [J]. IEEE ACCESS,2020,8:52173-52180.
APA Yu, Tieying,Chen, Min,&Wang, Chunde.(2020).An Improved Method for Identification of Pre-miRNA in < italic > Drosophila .IEEE ACCESS,8,52173-52180.
MLA Yu, Tieying,et al."An Improved Method for Identification of Pre-miRNA in < italic > Drosophila ".IEEE ACCESS 8(2020):52173-52180.

入库方式： OAI收割

来源：烟台海岸带研究所

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