Interdisciplinary Program in Statistics and Data Science, University of Arizona, Tucson, AZ, 85721, USA.
College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA.
Commun Biol. 2024 Apr 17;7(1):469. doi: 10.1038/s42003-024-06172-y.
Understanding gene expression in different cell types within their spatial context is a key goal in genomics research. SPADE (SPAtial DEconvolution), our proposed method, addresses this by integrating spatial patterns into the analysis of cell type composition. This approach uses a combination of single-cell RNA sequencing, spatial transcriptomics, and histological data to accurately estimate the proportions of cell types in various locations. Our analyses of synthetic data have demonstrated SPADE's capability to discern cell type-specific spatial patterns effectively. When applied to real-life datasets, SPADE provides insights into cellular dynamics and the composition of tumor tissues. This enhances our comprehension of complex biological systems and aids in exploring cellular diversity. SPADE represents a significant advancement in deciphering spatial gene expression patterns, offering a powerful tool for the detailed investigation of cell types in spatial transcriptomics.
理解不同细胞类型在其空间背景下的基因表达是基因组学研究的一个关键目标。我们提出的 SPADE(空间去卷积)方法通过将空间模式纳入细胞类型组成的分析中来解决这个问题。该方法结合了单细胞 RNA 测序、空间转录组学和组织学数据,以准确估计不同位置的细胞类型比例。我们对合成数据的分析表明,SPADE 能够有效地辨别细胞类型特异性的空间模式。当应用于真实数据集时,SPADE 提供了对细胞动态和肿瘤组织组成的深入了解。这增强了我们对复杂生物系统的理解,并有助于探索细胞多样性。SPADE 代表了破译空间基因表达模式的重大进展,为空间转录组学中对细胞类型的详细研究提供了强大的工具。
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