Tissue Expression Difference between mRNAs and lncRNAs
文献类型：期刊论文
| 作者 | Chen, Lei1,4,5; Wang, Shaopeng4; Cai, Yu-Dong4; Liu, Min1; Zhang, Yu-Hang3; Huang, Tao3; Pan, Xiaoyong2; , |
| 刊名 | INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
 |
| 出版日期 | 2018 |
| 卷号 | 19期号:11页码:3416 |
| 关键词 | mRNA lncRNA expression specificity cell type feature selection |
| ISSN号 | 1422-0067 |
| DOI | 10.3390/ijms19113416 |
| 文献子类 | Article |
| 英文摘要 | Messenger RNA (mRNA) and long noncoding RNA (lncRNA) are two main subgroups of RNAs participating in transcription regulation. With the development of next generation sequencing, increasing lncRNAs are identified. Many hidden functions of lncRNAs are also revealed. However, the differences in lncRNAs and mRNAs are still unclear. For example, we need to determine whether lncRNAs have stronger tissue specificity than mRNAs and which tissues have more lncRNAs expressed. To investigate such tissue expression difference between mRNAs and lncRNAs, we encoded 9339 lncRNAs and 14,294 mRNAs with 71 expression features, including 69 maximum expression features for 69 types of cells, one feature for the maximum expression in all cells, and one expression specificity feature that was measured as Chao-Shen-corrected Shannon's entropy. With advanced feature selection methods, such as maximum relevance minimum redundancy, incremental feature selection methods, and random forest algorithm, 13 features presented the dissimilarity of lncRNAs and mRNAs. The 11 cell subtype features indicated which cell types of the lncRNAs and mRNAs had the largest expression difference. Such cell subtypes may be the potential cell models for lncRNA identification and function investigation. The expression specificity feature suggested that the cell types to express mRNAs and lncRNAs were different. The maximum expression feature suggested that the maximum expression levels of mRNAs and lncRNAs were different. In addition, the rule learning algorithm, repeated incremental pruning to produce error reduction algorithm, was also employed to produce effective classification rules for classifying lncRNAs and mRNAs, which gave competitive results compared with random forest and could give a clearer picture of different expression patterns between lncRNAs and mRNAs. Results not only revealed the heterogeneous expression pattern of lncRNA and mRNA, but also gave rise to the development of a new tool to identify the potential biological functions of such RNA subgroups. |
| 学科主题 | Biochemistry & Molecular Biology ; Chemistry |
| WOS关键词 | LONG NONCODING RNAS ; WHITE BLOOD-CELL ; GENE-EXPRESSION ; FEATURE-SELECTION ; MOLECULAR FRAGMENTS ; AMINO-ACIDS ; STEM-CELLS ; PROTEIN ; TRANSCRIPTION ; CANCER |
| 语种 | 英语 |
| WOS记录号 | WOS:000451528500132 |
| 出版者 | MDPI |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.144/handle/331004/801]  |
| 专题 | 中国科学院上海生命科学研究院营养科学研究所 |
| 作者单位 | 1.Shanghai Maritime Univ, Coll Informat Engn, Shanghai 201306, Peoples R China; 2.Erasmus MC, Dept Med Informat, NL-3000 CA Rotterdam, Netherlands, 3.Chinese Acad Sci, Shanghai Inst Biol Sci, Inst Hlth Sci, Shanghai 200031, Peoples R China; 4.Shanghai Univ, Sch Life Sci, Shanghai 200444, Peoples R China; 5.East China Normal Univ, Shanghai Key Lab PMMP, Shanghai 200241, Peoples R China; |
| 推荐引用方式 GB/T 7714 | Chen, Lei,Wang, Shaopeng,Cai, Yu-Dong,et al. Tissue Expression Difference between mRNAs and lncRNAs[J]. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,2018,19(11):3416. |
| APA | Chen, Lei.,Wang, Shaopeng.,Cai, Yu-Dong.,Liu, Min.,Zhang, Yu-Hang.,...&,.(2018).Tissue Expression Difference between mRNAs and lncRNAs.INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES,19(11),3416. |
| MLA | Chen, Lei,et al."Tissue Expression Difference between mRNAs and lncRNAs".INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES 19.11(2018):3416. |
入库方式： OAI收割
来源：上海营养与健康研究所
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