3Scover: Identifying Safeguard TF from Cell Type-TF Specificity Network by an Extended Minimum Set Cover Model

doi:10.1016/j.isci.2020.101227

CSpace > 应用数学研究所

	3Scover: Identifying Safeguard TF from Cell Type-TF Specificity Network by an Extended Minimum Set Cover Model
	Yuan, Qiuyue 1,2,3,4; Wang, Yong1,2,3,4
	2020-06-26
发表期刊	ISCIENCE
卷号	23 期号:6 页码:31
摘要	Transcription 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.
DOI	10.1016/j.isci.2020.101227
收录类别	SCI
语种	英语
资助项目	Shanghai 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研究方向	Science & Technology - Other Topics
WOS类目	Multidisciplinary Sciences
WOS记录号	WOS:000548211500001
出版者	CELL PRESS
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/51811
专题	应用数学研究所
通讯作者	Wang, Yong
作者单位	1.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
推荐引用方式 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.