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3Scover: Identifying Safeguard TF from Cell Type-TF Specificity Network by an Extended Minimum Set Cover Model
Yuan, Qiuyue1,2,3,4; Wang, Yong1,2,3,4
2020-06-26
Source PublicationISCIENCE
Volume23Issue:6Pages:31
AbstractTranscription factors (TFs) define cellular identity either by activating target cell program or by silencing donor program as demonstrated by intensive cell reprogramming studies. Here, we propose an extended minimum set cover model with stable selection (3Scover) to systematically identify silencing TFs, named safeguard TFs, from omics data. First, a cell type-TF specificity network is constructed to systematically link cell types with their specifically expressed TFs. Then we search the minimum TF set to cover this network with "many but one specificity" characteristic and integrate many subsampling models for a stable solution. 3Scover identified 30 safeguard TFs in human and mouse. These safeguard TFs are significantly enriched in the experimentally discovered reprogramming panel with their protein-protein interactors. In addition, they tend to interact closely with chromatin regulators, negatively regulate transcription, and function earlier in development. Collectively, 3Scover allows us to probe master TFs and combinatorial regulation in controlling cell identity.
DOI10.1016/j.isci.2020.101227
Indexed BySCI
Language英语
Funding ProjectShanghai Municipal Science and Technology Major Project[2017SHZDZX01] ; CAS Light of West China Program[xbzg-zdsys-201913] ; National Key R&D Program of China[2017YFC0908400] ; National Natural Science Foundation of China (NSFC)[11871463] ; National Natural Science Foundation of China (NSFC)[61671444] ; National Natural Science Foundation of China (NSFC)[61621003]
WOS Research AreaScience & Technology - Other Topics
WOS SubjectMultidisciplinary Sciences
WOS IDWOS:000548211500001
PublisherCELL PRESS
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Document Type期刊论文
Identifierhttp://ir.amss.ac.cn/handle/2S8OKBNM/51811
Collection应用数学研究所
Corresponding AuthorWang, Yong
Affiliation1.Chinese Acad Sci, Acad Math & Syst Sci, NCMIS, CEMS,MDIS, Beijing 100190, Peoples R China
2.Univ Chinese Acad Sci, Sch Math Sci, Beijing 100049, Peoples R China
3.Chinese Acad Sci, Ctr Excellence Anim Evolut & Genet, Kunming 650223, Yunnan, Peoples R China
4.Chinese Acad Sci, Univ Chinese Acad Sci, Hangzhou Inst Adv Study, Key Lab Syst Biol, Hangzhou 310024, Peoples R China
Recommended Citation
GB/T 7714
Yuan, Qiuyue,Wang, Yong. 3Scover: Identifying Safeguard TF from Cell Type-TF Specificity Network by an Extended Minimum Set Cover Model[J]. ISCIENCE,2020,23(6):31.
APA Yuan, Qiuyue,&Wang, Yong.(2020).3Scover: Identifying Safeguard TF from Cell Type-TF Specificity Network by an Extended Minimum Set Cover Model.ISCIENCE,23(6),31.
MLA Yuan, Qiuyue,et al."3Scover: Identifying Safeguard TF from Cell Type-TF Specificity Network by an Extended Minimum Set Cover Model".ISCIENCE 23.6(2020):31.
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