Deciphering the Spatial Modular Patterns of Tissues by Integrating Spatial and Single-Cell Transcriptomic Data

doi:10.1089/cmb.2021.0617

CSpace > 应用数学研究所

	Deciphering the Spatial Modular Patterns of Tissues by Integrating Spatial and Single-Cell Transcriptomic Data
	Shan, Xu 1; Chen, Jinyu 2; Dong, Kangning3 ; Zhou, Wei 1; Zhang, Shihua3,4,5,6,7
	2022-06-21
发表期刊	JOURNAL OF COMPUTATIONAL BIOLOGY
ISSN	1066-5277
页码	14
摘要	Single-cell RNA sequencing (scRNA-seq) provides a powerful tool to analyze the expression level of tissues at a cellular resolution. However, it could not capture the spatial organization of cells in a tissue. The spatially resolved transcriptomics technologies (ST) have been developed to address this issue. However, the emerging STs are still inefficient at single-cell resolution and/or fail to capture the sufficient reads. To this end, we adopted a partial least squares-based method (spatial modular patterns [SpaMOD]) to simultaneously integrate the two data modalities, as well as the networks related to cells and spots, to identify the cell-spot comodules for deciphering the SpaMOD of tissues. We applied SpaMOD to three paired scRNA-seq and ST datasets, derived from the mouse brain, granuloma, and pancreatic ductal adenocarcinoma, respectively. The identified cell-spot comodules provide detailed biological insights into the spatial relationships between cell populations and their spatial locations in the tissue.
关键词	data integration single-cell transcriptomics spatial modular patterns spatial transcriptomics
DOI	10.1089/cmb.2021.0617
收录类别	SCI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Computer Science, Interdisciplinary Applications ; Mathematical & Computational Biology ; Statistics & Probability
WOS记录号	WOS:000813901800001
出版者	MARY ANN LIEBERT, INC
引用统计
文献类型	期刊论文
条目标识符	http://ir.amss.ac.cn/handle/2S8OKBNM/61248
专题	应用数学研究所
通讯作者	Zhang, Shihua
作者单位	1.Yunnan Univ, Department Software Engn, Kunming, Peoples R China 2.Beijing Univ Technol, Fac Sci, College Stat & Data Sci, Beijing, Peoples R China 3.Chinese Acad Sci, Acad Math & Syst Sci, CEMS, RCSDS,NCMIS, Beijing, Peoples R China 4.Univ Chinese Acad Sci, School Math Sci, Beijing, Peoples R China 5.Chinese Acad Sci, Center Excellence Anim Evolut & Genet, Kunming, Peoples R China 6.Univ Chinese Acad Sci, Hangzhou Inst Adv Study, Chinese Acad Sci, Key Lab Syst Biol, Hangzhou, Peoples R China 7.Chinese Acad Sci, Acad Math & Syst Sci, CEMS, RCSDS,NCMIS, Beijing 100190, Peoples R China
推荐引用方式 GB/T 7714	Shan, Xu,Chen, Jinyu,Dong, Kangning,et al. Deciphering the Spatial Modular Patterns of Tissues by Integrating Spatial and Single-Cell Transcriptomic Data[J]. JOURNAL OF COMPUTATIONAL BIOLOGY,2022:14.
APA	Shan, Xu,Chen, Jinyu,Dong, Kangning,Zhou, Wei,&Zhang, Shihua.(2022).Deciphering the Spatial Modular Patterns of Tissues by Integrating Spatial and Single-Cell Transcriptomic Data.JOURNAL OF COMPUTATIONAL BIOLOGY,14.
MLA	Shan, Xu,et al."Deciphering the Spatial Modular Patterns of Tissues by Integrating Spatial and Single-Cell Transcriptomic Data".JOURNAL OF COMPUTATIONAL BIOLOGY (2022):14.