SCING:从单细胞和空间转录组学推断出强大的,可解释的基因调节网络
Russell Littman1,2, Michael Cheng1,2, Ning Wang1
1Department of Integrative Biology & Physiology, UCLA, Los Angeles, CA, USA.
iScience
|July 12, 2023
概括
从单细胞和空间转录组学数据中,SCING准确地推断出基因调节网络 (GRNs). 这种新方法改进了了解细胞功能和疾病机制的现有方法.
科学领域:
- 基因组学就是基因组学.
- 计算生物学 计算生物学
- 系统生物学 系统生物学
背景情况:
- 基因调控网络 (GRN) 的推断对于理解生物系统和疾病至关重要.
- 目前用于GRN推断的单细胞RNA测序 (scRNA-seq) 方法在准确性和速度方面存在局限性.
研究的目的:
- 引入单细胞集成基因调控网络推断 (SCING),一种用于强大的GRN识别的新型计算方法.
- 为了提高GRN推断的准确性和可解释性,使用各种转录学数据.
主要方法:
- 开发了SCING,一种结合梯度增强和相互信息的方法.
- 将SCING应用于单细胞RNA测序 (scRNA-seq),单核RNA测序 (snRNA-seq) 和空间转录组学数据.
- 使用Perturb-seq数据集,持有数据和小鼠细胞地图,验证了SCING.
主要成果:
- 与现有的GRN推断方法相比,SCING显示出更高的准确性和生物解释性.
- 在人类阿尔茨海默病和小鼠模型中,SCING成功识别了特定疾病的子网络.
- 该方法本质上纠正批量效应,并揭示空间转录学洞察力.
结论:
- SCING为跨多种转录学模式的基因调控网络推断提供了一个强大而准确的平台.
- SCING提高了对细胞生理学和疾病发病的理解,特别是在像阿尔茨海默氏症这样的复杂疾病中.
更多相关视频
09:19Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
Published on: July 6, 2022
5.0K
09:34A Combinatorial Single-cell Approach to Characterize the Molecular and Immunophenotypic Heterogeneity of Human Stem and Progenitor Populations
Published on: October 25, 2018
6.7K
相关概念视频
02:24Ribosome Profiling
3.6K
Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
3.6K
01:58Cell Specific Gene Expression
13.6K
Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
13.6K
01:23Regulation of Expression at Multiple Steps
945
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...
945
02:33Combinatorial Gene Control
8.4K
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...
8.4K