KMS Of Academy of mathematics and systems sciences, CAS
| Annotating regulatory elements by heterogeneous network embedding | |
Lu, Yurun1,2; Feng, Zhanying1,2; Zhang, Songmao1 ; Wang, Yong1,2,3,4
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| 2022-03-24 | |
| Source Publication | BIOINFORMATICS
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| ISSN | 1367-4803 |
| Pages | 13 |
| Abstract | 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. |
| DOI | 10.1093/bioinformatics/btac185 |
| Indexed By | SCI |
| Language | 英语 |
| Funding Project | 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 Research Area | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics |
| WOS Subject | Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability |
| WOS ID | WOS:000787442000001 |
| Publisher | OXFORD UNIV PRESS |
| Citation statistics | |
| Document Type | 期刊论文 |
| Identifier | http://ir.amss.ac.cn/handle/2S8OKBNM/60394 |
| Collection | 应用数学研究所 数学所 |
| Corresponding Author | Lu, Yurun; Wang, Yong |
| Affiliation | 1.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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