使用空间转录组学重建空间感知受体-TF-目标信号级联的协议
Yao Li1, Xiaobin Liu2, Xinkai Yan3
1BGI Research, Qingdao 266555, China; Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hong Kong 999077, China.
STAR protocols
|December 12, 2025
概括
这项研究引入了SpaGRN,这是一种新的基因调节网络分析方法,它考虑了空间信息. 它重建了组织中的空间感知信号通路,改善了对复杂生物系统的理解.
科学领域:
- 空间转录组学 空间转录组学
- 系统生物学 系统生物学
- 生物信息学是一种生物信息学.
背景情况:
- 基因调节网络 (GRNs) 对于细胞功能至关重要.
- 现有的GRN推断方法往往忽视了转录学数据中的空间上下文.
- 了解空间关系对于复杂的组织如胚胎和瘤至关重要.
研究的目的:
- 提出一个用于重建空间感知基因调节网络的新方案.
- 整合细胞外信号传输和空间依赖性,以改善GRN推断.
- 为了使复杂的生物样本中信号通路的系统映射.
主要方法:
- 使用SpaGRN统计框架.
- 整合空间自相关性和共同表达分析.
- 执行cis调节动机丰富和与受体相关的调节推理.
- 采用3D可视化技术用于空间数据表示.
主要成果:
- 成功重建受体-转录因子-目标调节级联与空间意识.
- 展示SpaGRN在分析复杂组织方面的能力.
- 开发一个用于空间GRN推断的综合协议.
结论:
- SpaGRN为空间解析的GRN分析提供了一个强大的框架.
- 该协议有助于更深入地了解发育和疾病背景下的信号通路.
- 这种方法通过结合空间约束来增强空间转录组学数据的分析.
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