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Annotating regulatory elements by heterogeneous network embedding

文献类型：期刊论文

作者Lu, Yurun3,4; Feng, Zhanying3,4; Zhang, Songmao4; Wang, Yong1,2,3,4
刊名BIOINFORMATICS
出版日期2022-03-24
页码13
ISSN号1367-4803
DOI10.1093/bioinformatics/btac185
英文摘要Motivation: Regulatory elements (REs), such as enhancers and promoters, are known as regulatory sequences functional in a heterogeneous regulatory network to control gene expression by recruiting transcription regulators and carrying genetic variants in a context specific way. Annotating those REs relies on costly and labor-intensive next-generation sequencing and RNA-guided editing technologies in many cellular contexts. Results: We propose a systematic Gene Ontology Annotation method for Regulatory Elements (RE-GOA) by leveraging the powerful word embedding in natural language processing. We first assemble a heterogeneous network by integrating context specific regulations, protein-protein interactions and gene ontology (GO) terms. Then we perform network embedding and associate regulatory elements with GO terms by assessing their similarity in a low dimensional vector space. With three applications, we show that RE-GOA outperforms existing methods in annotating TFs' binding sites from ChIP-seq data, in functional enrichment analysis of differentially accessible peaks from ATAC-seq data, and in revealing genetic correlation among phenotypes from their GWAS summary statistics data.
资助项目National Key Research and Development Program of China[2020YFA0712402] ; Strategic Priority Research Program of the Chinese Academy of Sciences[XDPB17] ; National Natural Science Foundation of China[12025107] ; National Natural Science Foundation of China[11871463] ; National Natural Science Foundation of China[61621003] ; National Natural Science Foundation of China[11688101]
WOS研究方向Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
语种英语
WOS记录号WOS:000787442000001
出版者OXFORD UNIV PRESS
源URL[http://ir.amss.ac.cn/handle/2S8OKBNM/60393]  
专题应用数学研究所
数学所
通讯作者Lu, Yurun; Wang, Yong
作者单位1.Univ Chinese Acad Sci, Hangzhou Inst Adv Study, Chinese Acad Sci, Key Lab Syst Biol, Hangzhou 330106, Peoples R China
2.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China
3.Univ Chinese Acad Sci, Chinese Acad Sci, Sch Math, Beijing 100049, Peoples R China
4.Chinese Acad Sci, Acad Math & Syst Sci, CEMS, NCMIS,HCMS,MADIS, Beijing 100190, Peoples R China
推荐引用方式
GB/T 7714		 Lu, Yurun,Feng, Zhanying,Zhang, Songmao,et al. Annotating regulatory elements by heterogeneous network embedding[J]. BIOINFORMATICS,2022:13.
APA Lu, Yurun,Feng, Zhanying,Zhang, Songmao,&Wang, Yong.(2022).Annotating regulatory elements by heterogeneous network embedding.BIOINFORMATICS,13.
MLA Lu, Yurun,et al."Annotating regulatory elements by heterogeneous network embedding".BIOINFORMATICS (2022):13.

入库方式： OAI收割

来源：数学与系统科学研究院

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