一种检测细胞间相关性的空间染色质可及性模式的方法

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-12-30 DOI:10.1186/s13059-024-03458-6

Xiaoyang Chen, Keyi Li, Xiaoqing Wu, Zhen Li, Qun Jiang, Xuejian Cui, Zijing Gao, Yanhong Wu, Rui Jiang

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引用次数: 0

摘要

空间表观基因组技术能够同时捕获组织切片内细胞的空间位置和染色质可及性。识别显示空间变异和细胞异质性的峰是表征复杂组织空间染色质可及性景观的关键分析任务。在这里，我们提出了一个高效的迭代模型Descart，用于基于细胞间相关性图的空间变量峰识别。通过全面的基准测试，我们证明了Descart在揭示细胞异质性和捕获组织结构方面的优势。利用细胞间相关性图，Descart展示了其去噪数据、识别峰值模块和检测基因峰相互作用的潜力。

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Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations

Spatial epigenomic technologies enable simultaneous capture of spatial location and chromatin accessibility of cells within tissue slices. Identifying peaks that display spatial variation and cellular heterogeneity is the key analytic task for characterizing the spatial chromatin accessibility landscape of complex tissues. Here, we propose an efficient and iterative model, Descart, for spatially variable peaks identification based on the graph of inter-cellular correlations. Through the comprehensive benchmarking, we demonstrate the superiority of Descart in revealing cellular heterogeneity and capturing tissue structure. Utilizing the graph of inter-cellular correlations, Descart shows its potential to denoise data, identify peak modules, and detect gene-peak interactions.

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.