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CEA: Combination-based gene set functional enrichment analysis
Sun, Duanchen1,2; Liu, Yinliang1,2; Zhang, Xiang-Sun1; Wu, Ling-Yun1,2
2018-08-30
Source PublicationSCIENTIFIC REPORTS
ISSN2045-2322
Volume8Pages:13
AbstractFunctional 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/.
DOI10.1038/s41598-018-31396-4
Language英语
Funding ProjectStrategic 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 Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000443160800025
PublisherNATURE PUBLISHING GROUP
Citation statistics
Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/31177
Collection应用数学研究所
Affiliation1.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
Recommended Citation
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.
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