Tumor origin detection with tissue-specific miRNA and DNA methylation markers
文献类型：期刊论文
| 作者 | Tang, Wei1,2; Wan, Shixiang1; Zou, Quan1; Yang, Zhen3; Teschendorff, Andrew E.3; Teschendorff, Andrew E.4; , |
| 刊名 | BIOINFORMATICS
 |
| 出版日期 | 2018 |
| 卷号 | 34期号:3页码:398-406 |
| 关键词 | CARF chemical biology NC043 small molecule Wnt signaling |
| ISSN号 | 1367-4803 |
| DOI | 10.1093/bioinformatics/btx622 |
| 文献子类 | Article |
| 英文摘要 | Motivation: A clear identification of the primary site of tumor is of great importance to the next targeted site-specific treatments and could efficiently improve patient's overall survival. Even though many classifiers based on gene expression had been proposed to predict the tumor primary, only a few studies focus on using DNA methylation (DNAm) profiles to develop classifiers, and none of them compares the performance of classifiers based on different profiles. Results: We introduced novel selection strategies to identify highly tissue-specific CpG sites and then used the random forest approach to construct the classifiers to predict the origin of tumors. We also compared the prediction performance by applying similar strategy on miRNA expression profiles. Our analysis indicated that these classifiers had an accuracy of 96.05% (Maximum-Relevance-Maximum-Distance: 90.02-99.99%) or 95.31% (principal component analysis: 79.82-99.91%) on independent DNAm datasets, and an overall accuracy of 91.30% (range 79.33-98.74%) on independent miRNA test sets for predicting tumor origin. This suggests that our feature selection methods are very effective to identify tissue-specific biomarkers and the classifiers we developed can efficiently predict the origin of tumors. We also developed a user-friendly webserver that helps users to predict the tumor origin by uploading miRNA expression or DNAm profile of their interests. |
| 学科主题 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics |
| WOS关键词 | CELL-PROLIFERATION ; UNKNOWN PRIMARY ; CANCER ; MICRORNAS ; IDENTIFICATION ; ASSOCIATIONS ; CARCINOMA ; IDENTIFY |
| 语种 | 英语 |
| WOS记录号 | WOS:000423978700006 |
| 出版者 | OXFORD UNIV PRESS |
| 版本 | 出版稿 |
| 源URL | [http://202.127.25.144/handle/331004/1037]  |
| 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.Tianjin Univ, Sch Chem Engn, Sch Comp Sci & Technol, Tianjin 300050, Peoples R China; 2.Tianjin Univ, Sch Chem Engn, Dept Biol Engn, Tianjin 300050, Peoples R China; 3.CAS MPG Partner Inst Computat Biol, Key Lab Computat Biol, Shanghai 200031, Peoples R China; 4.UCL, UCL Canc Inst, Stat Canc Genom, Paul OGorman Bldg, London WC1E 6BT, England, |
| 推荐引用方式 GB/T 7714 | Tang, Wei,Wan, Shixiang,Zou, Quan,et al. Tumor origin detection with tissue-specific miRNA and DNA methylation markers[J]. BIOINFORMATICS,2018,34(3):398-406. |
| APA | Tang, Wei.,Wan, Shixiang.,Zou, Quan.,Yang, Zhen.,Teschendorff, Andrew E..,...&,.(2018).Tumor origin detection with tissue-specific miRNA and DNA methylation markers.BIOINFORMATICS,34(3),398-406. |
| MLA | Tang, Wei,et al."Tumor origin detection with tissue-specific miRNA and DNA methylation markers".BIOINFORMATICS 34.3(2018):398-406. |
入库方式： OAI收割
来源：上海营养与健康研究所
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