凯格尼:知识图增强基因调控网络推断框架
Pengxiao Li1, Lin Li1, Jingminjie Nan2
1Shanghai Center for Systems Biomedicine, Key Laboratory of Systems Biomedicine (Ministry of Education), Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
Genome biology
|September 22, 2025
概括
我们开发了KEGNI,这是一个用于从单细胞RNA测序数据中推断基因调节网络 (GRNs) 的新框架. 凯格尼利用知识图来提高识别基因调节关系和驱动基因的准确性.
科学领域:
- 计算生物学 计算生物学
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 基因调节网络 (GRNs) 对于理解细胞机制至关重要.
- 推断细胞类型特定的GRNs是必不可少的,但在复杂的生物数据中具有挑战性.
- 现有的方法往往缺乏有效地整合先前的生物知识的能力.
研究的目的:
- 介绍KEGNI (知识图增强基因调控网络推理),这是GRN推理的新框架.
- 用单细胞RNA测序 (scRNA-seq) 数据提高GRN推断的准确性和可解释性.
- 证明KEGNI在识别驱动基因和阐明监管机制方面的能力.
主要方法:
- 凯格尼采用以知识为导向的方法,使用图形自编码器.
- 它集成了一个知识图,以捕捉和推断基因调节关系.
- 该框架旨在处理scRNA-seq数据,并有可能对scRNA-seq和scATAC-seq数据进行配对.
主要成果:
- 在GRN推断中,KEGNI在现有方法中表现优越.
- 该框架成功地在不同的细胞环境中识别了驱动基因.
- 凯格尼有效地利用综合知识阐明了复杂的监管机制.
结论:
- 凯格尼提供了一种强大而准确的方法来推断细胞类型特定的GRNs.
- 以知识为导向的方法增强了从scRNA-seq数据对基因调节的理解.
- 凯格尼的模块化设计允许灵活整合各种知识来源,用于各种应用.
相关概念视频
Protein Networks
4.5K
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,...
4.5K
Protein Networks
2.8K
2.8K
Constitutive and Regulated Gene Expression
944
Gene expression in prokaryotes is governed by constitutive and regulated systems, allowing cells to balance the production of essential proteins with adaptive responses to environmental changes.Constitutive Gene ExpressionConstitutive, or housekeeping, genes are continuously expressed as they encode proteins vital for fundamental cellular processes. These include enzymes for glycolysis, ribosomal components for protein synthesis, and proteins involved in DNA replication. Their constant...
944
Combinatorial Gene Control
9.5K
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...
9.5K
Genome-wide Association Studies-GWAS
15.3K
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...
15.3K
Cooperative Binding of Transcription Regulators
7.2K
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
7.2K


