CEA: Combination-based gene set functional enrichment analysis
文献类型：期刊论文
| 作者 | Sun, Duanchen1,2; Liu, Yinliang1,2; Zhang, Xiang-Sun1 ; Wu, Ling-Yun1,2
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| 刊名 | SCIENTIFIC REPORTS
 |
| 出版日期 | 2018-08-30 |
| 卷号 | 8页码:13 |
| ISSN号 | 2045-2322 |
| DOI | 10.1038/s41598-018-31396-4 |
| 英文摘要 | Functional enrichment analysis is a fundamental and challenging task in bioinformatics. Most of the current enrichment analysis approaches individually evaluate functional terms and often output a list of enriched terms with high similarity and redundancy, which makes it difficult for downstream studies to extract the underlying biological interpretation. In this paper, we proposed a novel framework to assess the performance of combination-based enrichment analysis. Using this framework, we formulated the enrichment analysis as a multi-objective combinatorial optimization problem and developed the CEA (Combination-based Enrichment Analysis) method. CEA provides the whole landscape of term combinations; therefore, it is a good benchmark for evaluating the current state-of-the-art combination-based functional enrichment methods in a comprehensive manner. We tested the effectiveness of CEA on four published microarray datasets. Enriched functional terms identified by CEA not only involve crucial biological processes of related diseases, but also have much less redundancy and can serve as a preferable representation for the enriched terms found by traditional single-term-based methods. CEA has been implemented in the R package CopTea and is available at http://github.com/wulingyun/CopTea/. |
| 资助项目 | Strategic Priority Research Program of the Chinese Academy of Sciences[XDB13040600] ; National Natural Science Foundation of China[11631014] ; National Natural Science Foundation of China[91730301] ; National Natural Science Foundation of China[11661141019] |
| WOS研究方向 | Science & Technology - Other Topics |
| 语种 | 英语 |
| WOS记录号 | WOS:000443160800025 |
| 出版者 | NATURE PUBLISHING GROUP |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/31176]  |
| 专题 | 应用数学研究所 |
| 通讯作者 | Wu, Ling-Yun |
| 作者单位 | 1.Chinese Acad Sci, Acad Math & Syst Sci, IAM, MADIS,NCMIS, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China |
| 推荐引用方式 GB/T 7714 | Sun, Duanchen,Liu, Yinliang,Zhang, Xiang-Sun,et al. CEA: Combination-based gene set functional enrichment analysis[J]. SCIENTIFIC REPORTS,2018,8:13. |
| APA | Sun, Duanchen,Liu, Yinliang,Zhang, Xiang-Sun,&Wu, Ling-Yun.(2018).CEA: Combination-based gene set functional enrichment analysis.SCIENTIFIC REPORTS,8,13. |
| MLA | Sun, Duanchen,et al."CEA: Combination-based gene set functional enrichment analysis".SCIENTIFIC REPORTS 8(2018):13. |
入库方式： OAI收割
来源：数学与系统科学研究院
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