MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting

doi:10.1093/bib/bbab235

CSpace > 应用数学研究所

	MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting
	Zou, Meng 1; Duren, Zhana 2; Yuan, Qiuyue 3; Li, Henry 4; Hutchins, Andrew Paul 5; Wong, Wing Hung 6; Wang, Yong7
	2021-11-01
发表期刊	BRIEFINGS IN BIOINFORMATICS
ISSN	1467-5463
卷号	22 期号:6 页码:14
摘要	Multi-omics data allow us to select a small set of informative markers for the discrimination of specific cell types and study of cellular heterogeneity. However, it is often challenging to choose an optimal marker panel from the high-dimensional molecular profiles for a large amount of cell types. Here, we propose a method called Mixed Integer programming Model to Identify Cell type-specific marker panel (MIMIC). MIMIC maintains the hierarchical topology among different cell types and simultaneously maximizes the specificity of a fixed number of selected markers. MIMIC was benchmarked on the mouse ENCODE RNA-seq dataset, with 29 diverse tissues, for 43 surface markers (SMs) and 1345 transcription factors (TFs). MIMIC could select biologically meaningful markers and is robust for different accuracy criteria. It shows advantages over the standard single gene-based approaches and widely used dimensional reduction methods, such as multidimensional scaling and t-SNE, both in accuracy and in biological interpretation. Furthermore, the combination of SMs and TFs achieves better specificity than SMs or TFs alone. Applying MIMIC to a large collection of 641 RNA-seq samples covering 231 cell types identifies a panel of TFs and SMs that reveal the modularity of cell type association networks. Finally, the scalability of MIMIC is demonstrated by selecting enhancer markers from mouse ENCODE data. MIMIC is freely available at https://github.com/MengZou1/MIMIC.
关键词	cell type-specific marker TFs surface markers dimension reduction hierarchical topology
DOI	10.1093/bib/bbab235
收录类别	SCI
语种	英语
资助项目	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[12001215] ; Fundamental Research Funds for Central Universities[5003011023] ; National Institutes of Health[P50HG007735] ; National Institutes of Health[R01HG007834] ; National Institutes of Health[R01HG010359] ; National Key R&D Program of China[2017YFC0908400] ; National Key R&D Program of China[2020YFA0712402]
WOS研究方向	Biochemistry & Molecular Biology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Mathematical & Computational Biology
WOS记录号	WOS:000733325700105
出版者	OXFORD UNIV 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/59770
专题	应用数学研究所
通讯作者	Wang, Yong
作者单位	1.Huazhong Univ Sci & Technol, Dept Math, Beijing, Peoples R China 2.Clemson Univ, Dept Genet & Biochem, Clemson, SC 29631 USA 3.Chinese Acad Sci, Acad Math & Syst Sci, Beijing, Peoples R China 4.Stanford Univ, Bio X Program, Dept Hlth Res & Policy, Stanford, CA 94305 USA 5.Southern Univ Sci & Technol, Beijing, Peoples R China 6.Stanford Univ, Bio X Program, Dept Biomed Data Sci, Dept Stat, Stanford, CA 94305 USA 7.Chinese Acad Sci, Acad Math & Syst Sci, Ctr Excellence Anim Evolut & Genet, Univ Chinese Acad Sci,CEMS,NCMIS,MDIS, Beijing, Peoples R China
推荐引用方式 GB/T 7714	Zou, Meng,Duren, Zhana,Yuan, Qiuyue,et al. MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting[J]. BRIEFINGS IN BIOINFORMATICS,2021,22(6):14.
APA	Zou, Meng.,Duren, Zhana.,Yuan, Qiuyue.,Li, Henry.,Hutchins, Andrew Paul.,...&Wang, Yong.(2021).MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting.BRIEFINGS IN BIOINFORMATICS,22(6),14.
MLA	Zou, Meng,et al."MIMIC: an optimization method to identify cell type-specific marker panel for cell sorting".BRIEFINGS IN BIOINFORMATICS 22.6(2021):14.