Deciphering the Spatial Modular Patterns of Tissues by Integrating Spatial and Single-Cell Transcriptomic Data
文献类型：期刊论文
| 作者 | Shan, Xu1; Chen, Jinyu2; Dong, Kangning3 ; Zhou, Wei1; Zhang, Shihua3,4,5,6,7
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| 刊名 | JOURNAL OF COMPUTATIONAL BIOLOGY
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| 出版日期 | 2022-06-21 |
| 页码 | 14 |
| ISSN号 | 1066-5277 |
| 关键词 | data integration single-cell transcriptomics spatial modular patterns spatial transcriptomics |
| DOI | 10.1089/cmb.2021.0617 |
| 英文摘要 | 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. |
| WOS研究方向 | Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Computer Science ; Mathematical & Computational Biology ; Mathematics |
| 语种 | 英语 |
| 出版者 | MARY ANN LIEBERT, INC |
| WOS记录号 | WOS:000813901800001 |
| 源URL | [http://ir.amss.ac.cn/handle/2S8OKBNM/61247]  |
| 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. |
入库方式： OAI收割
来源：数学与系统科学研究院
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