对基因相互作用进行自我监督的深度学习,以改善基因表达恢复
Qingyue Wei1, Md Tauhidul Islam2, Yuyin Zhou3
1Institute for Computational and Mathematical Engineering, Stanford University, Stanford, 94305 CA, USA.
Briefings in bioinformatics
|February 13, 2024
概括
这项研究引入了一种新的方法,通过利用基因-基因相互作用来改善单细胞RNA测序 (scRNA-seq) 中的基因表达赋值. 自主监督的深度学习方法提高了数据准确性,以获得更好的生物洞察力.
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:
- 单细胞RNA测序 (scRNA-seq) 提供了细胞水平的生物学见解,但由于遗漏的低基因表达值,它受到技术限制,导致基因计数不准确.
- 目前的归因方法,包括深度学习,往往无法可靠地归因基因表达,因为它们缺乏将基因与基因相互作用等生物知识纳入的机制.
研究的目的:
- 开发一种新的基因组数据分析框架,利用基因相互作用来更可靠地归算scRNA-seq数据.
- 通过提取和整合复杂的生物特征来改善独特的细胞模式的识别.
主要方法:
- 基因被重新定位成一个二维网格,空间反映了它们的互动关系.
- 自主监督的2D卷积神经网络被用来从空间配置的基因中提取上下文特征,在不需要标记数据集的情况下赋值遗漏值.
主要成果:
- 与现有方法相比,拟议的策略在基因表达赋值方面表现出优异的性能.
- 在模拟和真实scRNA-seq数据集上的广泛实验验证了该方法的有效性.
结论:
- 通过空间配置和自我监督学习利用基因相互作用显著提高了scRNA-seq数据中的基因表达赋值.
- 这种方法为分析单细胞基因组数据提供了更准确,更有生物学知识的方法,改善了细胞特征的发现.
相关概念视频
01:42What is Gene Expression?
Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
01:42What is Gene Expression?
Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
02:07Improving Translational Accuracy
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
01:36What is Gene Expression?
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then processed and...
02:07Improving Translational Accuracy
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...