scRDEN:单细胞动态基因排名差异表达网络和强大的轨迹推断推断
Han Zhang1, Wei Zhang1, Xiaoying Zheng2
1School of Mathematics and Physics, Wuhan Institute of Technology, Wuhan, 430073, China.
Scientific reports
|May 15, 2025
概括
该scRDEN框架准确地识别细胞亚群和基因表达网络,揭示细胞分化过程中的动态调控变化. 这种方法增强了对从单细胞RNA测序数据的转录调节和发育轨迹的理解.
科学领域:
- 计算生物学 计算生物学
- 基因组学就是基因组学.
- 发展生物学 发展生物学
背景情况:
- 单细胞RNA测序 (scRNA-seq) 能够在细胞水平上进行精确的基因表达分析.
- 了解细胞命运决定需要分析动态调节变化和推断分化轨迹.
- 现有的方法在全面分析转录异质性和发育路径方面面临挑战.
研究的目的:
- 引入scRDEN,一个强大的框架来推断细胞亚群和差异表达网络.
- 分析基因表达动态和沿着差异化轨迹的调节性变化.
- 提供关于细胞分化和发育过程中的转录调节的见解.
主要方法:
- scRDEN将不稳定的基因表达值转换为稳定的基因相互作用 (全球特征).
- 它提取差异表达顺序 (网络特征) 并集成多维缩减表达特征.
- 该框架分析基因表达,识别细胞亚群,并构建差异表达网络.
主要成果:
- 在五个scRNA-seq数据集中,scRDEN成功地确定了具有潜在标记基因的稳定细胞亚群.
- 它准确地测量了转录差异,以沿着差异化分支建立排列差异表达网络.
- 分析显示了网络多样性和集群系数的非单调趋势,与差异化成稳定函数相关.
结论:
- scRDEN为分析细胞分化轨迹和调控机制提供了一个强大的框架.
- 该方法为大规模,多批次轨迹推断和转录调节提供了新的见解.
- 在复杂的数据集上,scRDEN表现出了卓越的性能,包括小鼠牙状回路数据.
相关概念视频
01:58Cell Specific Gene Expression
4.5K
4.5K
02:05Gene Evolution - Fast or Slow?
2.8K
2.8K
01:23Regulation of Expression at Multiple Steps
850
The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
850
03:21RNA-seq
9.7K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
9.7K
02:26Protein Networks
3.9K
An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
3.9K