School of Electrical Engineering and Automation, Hefei University of Technology, Hefei, Anhui 230009, China.
School of Electrical Engineering and Automation, Hefei University of Technology, Hefei, Anhui 230009, China.
Comput Biol Chem. 2024 Oct;112:108127. doi: 10.1016/j.compbiolchem.2024.108127. Epub 2024 Jun 11.
Spatial transcriptomics, a groundbreaking field in cellular biology, faces the challenge of effectively deciphering complex spatial-temporal gene expression patterns. Traditional data analysis methods often fail to capture the intricate nuances of this data, limiting the depth of understanding in spatial distribution and gene interactions. In response, we present Spatial-Temporal Patterns for Downstream Analysis (STPDA), a sophisticated computational framework tailored for spatial transcriptomic data analysis. STPDA leverages high-resolution mapping to bridge the gap between genomics and histopathology, offering a comprehensive perspective on the spatial dynamics of gene expression within tissues. This approach enables a view of cellular function and organization, marking a paradigm shift in our comprehension of biological systems. By employing Autoregressive Moving Average (ARMA) and Long Short-Term Memory (LSTM) models, STPDA effectively deciphers both global and local spatio-temporal dynamics in cellular environments. This integration of spatial-temporal patterns for downstream analysis offers a transformative approach to spatial transcriptomics data analysis. STPDA excels in various single-cell analytical tasks, including the identification of ligand-receptor interactions and cell type classification. Its ability to harness spatial-temporal patterns not only matches but frequently surpasses the performance of existing state-of-the-art methods. To ensure widespread usability and impact, we have encapsulated STPDA in a scalable and accessible Python package, addressing single-cell tasks through advanced spatial-temporal pattern analysis. This development promises to enhance our understanding of cellular biology, offering novel insights and therapeutic strategies, and represents a substantial advancement in the field of spatial transcriptomics.
空间转录组学是细胞生物学领域的一个突破性领域,面临着有效破译复杂时空基因表达模式的挑战。传统数据分析方法往往无法捕捉到这些数据的复杂细微差别,限制了对空间分布和基因相互作用的深入理解。针对这一问题,我们提出了用于下游分析的时空模式(STPDA),这是一种针对空间转录组数据分析的复杂计算框架。STPDA 利用高分辨率映射来弥合基因组学和组织病理学之间的差距,为组织内基因表达的空间动态提供全面的视角。这种方法使我们能够观察细胞功能和组织,标志着我们对生物系统理解的范式转变。通过使用自回归移动平均(ARMA)和长短期记忆(LSTM)模型,STPDA 能够有效地破译细胞环境中的全局和局部时空动态。这种用于下游分析的时空模式的整合为空间转录组数据分析提供了一种变革性的方法。STPDA 在各种单细胞分析任务中表现出色,包括配体-受体相互作用的识别和细胞类型分类。它利用时空模式的能力不仅匹配,而且经常超过现有最先进方法的性能。为了确保广泛的可用性和影响力,我们将 STPDA 封装在一个可扩展和可访问的 Python 包中,通过高级时空模式分析来解决单细胞任务。这一发展有望增强我们对细胞生物学的理解,提供新的见解和治疗策略,并代表空间转录组学领域的重大进展。
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