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Annotating regulatory elements by heterogeneous network embedding
Lu, Yurun1,2; Feng, Zhanying1,2; Zhang, Songmao1; Wang, Yong1,2,3,4
Source PublicationBIOINFORMATICS
AbstractMotivation: 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.
Indexed BySCI
Funding ProjectNational 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 Research AreaBiochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS SubjectBiochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS IDWOS:000787442000001
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Document Type期刊论文
Corresponding AuthorLu, Yurun; Wang, Yong
Affiliation1.Chinese Acad Sci, Acad Math & Syst Sci, CEMS, NCMIS,HCMS,MADIS, Beijing 100190, Peoples R China
2.Univ Chinese Acad Sci, Chinese Acad Sci, Sch Math, Beijing 100049, Peoples R China
3.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China
4.Univ Chinese Acad Sci, Hangzhou Inst Adv Study, Chinese Acad Sci, Key Lab Syst Biol, Hangzhou 330106, Peoples R China
Recommended Citation
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.
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