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在基于单细胞成像的空间解析转录组学中基因计数正常化.

Lyla Atta1,2, Kalen Clifton1,2, Manjari Anant2,3

  • 1Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21218, USA.

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概括
此摘要是机器生成的。

基于成像的空间解析转录学 (im-SRT) 中的规范化方法可以扭曲结果. 使用代表组织生物学的基因面板对于可靠的im-SRT数据分析至关重要.

关键词:
规范化 规范化 规范化不同的表达方式,不同的表达方式.缩放因子是一个缩放因子.空间转录学 空间转录学

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科学领域:

  • 基因组学就是基因组学.
  • 生物信息学是一种生物信息学.
  • 计算生物学 计算生物学

背景情况:

  • 基于成像的空间解析转录组学 (im-SRT) 允许在固定的组织中进行高通量基因分析.
  • 在im-SRT中,规范化至关重要,以纠正技术变异并确保准确的生物信号解释.

研究的目的:

  • 研究不同基因计数正常化方法对im-SRT数据分析的影响.
  • 评估不同向基因组对正常化结果的影响.
  • 评估下游分析的可靠性,受标准化选择的影响.

主要方法:

  • 使用模拟基因面板,过度代表特定组织区域或细胞类型.
  • 用基因计数和非基因计数方法进行基因表达数据正常化.
  • 下游分析包括差异基因表达和空间变量基因分析进行了比较.

主要成果:

  • 基于基因计数的规范化方法以特定区域和细胞类型的方式对规范化的基因表达量产生了差异的影响.
  • 在下游分析中,规范化诱导的效应导致虚假阳性和虚假阴性结果.
  • 基于非基因计数的正常化 (例如细胞体积/面积) 并没有引入这些偏差.

结论:

  • 建议在可能的情况下使用基于基因计数的非基因计数规范化方法来处理im-SRT数据.
  • 强调在应用基因计数基础的正常化之前评估基因组的代表性.
  • 强调,规范化方法和基因组的选择显著影响im-SRT数据的生物学解释.