最佳运输通过基因速度估计揭示了动态的基因调节网络
Wenjun Zhao1,2, Erica Larschan3, Björn Sandstede1
1Division of Applied Mathematics, Brown University, Providence, Rhode Island, United States of America.
PLoS computational biology
|May 9, 2025
概括
通过使用最佳传输来估计基因速度,OTVelo推断出基因调节网络,即使有有限的测序数据. 这种方法揭示了跨时间点的动态基因调节,以增强生物洞察力.
科学领域:
- 计算生物学 计算生物学
- 系统生物学 系统生物学
- 基因组学就是基因组学.
背景情况:
- 推断基因调节网络对于理解生物系统至关重要.
- 基因表达数据是关键,但推断基因的动态是具有挑战性的.
- 基因速度 (变化速率) 增强了网络推断,但往往无法使用.
研究的目的:
- 引入OTVelo,一种用于推断基因调节网络的新方法.
- 使用最佳运输来估计基因速度,克服数据限制.
- 发现跨时间点的动态基因调节机制.
主要方法:
- OTVelo使用时间标记的单细胞基因表达数据.
- 通过最佳运输估计基因速度,以处理测序深度限制.
- 使用时间滞后相关性和格兰杰因果关系与规范线性回归推断基因调节.
主要成果:
- OTVelo成功地估计了基因速度,并推断了基因调节.
- 该方法揭示了动态机制,而不是静态网络.
- 在13个模拟和9个实验数据集上得到验证,证明了有效性.
结论:
- OTVelo提供了一种强大的方法,可以从时间序列单细胞数据中推断基因调节网络.
- 该方法有效地利用基因速度估计来提高网络推断的准确性.
- OTVelo推进了对生物系统中动态基因调节的理解.
相关概念视频
Gene Evolution - Fast or Slow?
2.8K
2.8K
Regulated mRNA Transport
2.8K
2.8K
Regulation of Expression at Multiple Steps
849
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...
849
Combinatorial Gene Control
8.2K
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
8.2K
Gene Flow
34.4K
Gene flow is the transfer of genes among populations, resulting from either the dispersal of gametes or from the migration of individuals.
34.4K
Regulation of Expression Occurs at Multiple Steps
22.0K
Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
22.0K


