CEA: Combination-based gene set functional enrichment analysis

doi:10.1038/s41598-018-31396-4

CORC > 数学与系统科学研究院 > 中国科学院数学与系统科学研究院 > 应用数学研究所

	CEA: Combination-based gene set functional enrichment analysis
	Sun, Duanchen 1,2; Liu, Yinliang 1,2; Zhang, Xiang-Sun 1; Wu, Ling-Yun1,2
刊名	SCIENTIFIC REPORTS
	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
出版者	NATURE PUBLISHING GROUP
WOS记录号	WOS:000443160800025
内容类型	期刊论文
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.