scPROTEIN:一个多功能深度图对比学习框架,用于嵌入单细胞蛋白质组的单细胞蛋白质组.
Wei Li1,2, Fan Yang2, Fang Wang2
1College of Artificial Intelligence, Nankai University, Tianjin, China.
Nature methods
|March 20, 2024
概括
scPROTEIN是单细胞蛋白组学分析的新框架. 它解决了诸如量化不确定性和批量效应等关键挑战,以改善数据解释.
科学领域:
- 蛋白质组学是指蛋白质组学.
- 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:
- 单细胞蛋白质组学为细胞过程提供了洞察力,但也面临着挑战.
- 定量的不确定性,缺少的数据,批量效应和噪音阻碍了分析.
- 现有的单细胞转录组方法对于蛋白质组数据是不够的.
研究的目的:
- 开发用于单细胞蛋白质组学数据分析的多功能框架.
- 在统一的方法中解决多种分析挑战.
- 提高单细胞蛋白质组数据的准确性和可解释性.
主要方法:
- 一个多任务的异回归模型用于不确定性估计.
- 图表对比学习用于细胞嵌入生成.
- 在一个统一的框架中整合不确定性和细胞嵌入.
主要成果:
- scPROTEIN有效地估计了的量化不确定性.
- 该框架成功地拒绝了蛋白质数据,并消除了批量效应.
- 它产生了强大的单细胞蛋白质特异性嵌入.
结论:
- scPROTEIN为单细胞蛋白质组学数据分析提供了一个全面的解决方案.
- 该框架在细胞聚类,批次校正和细胞类型注释方面表现出效率.
- scPROTEIN促进了对空间解析的蛋白质组数据的临床分析和探索.
相关概念视频
Proteomics
7.3K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
7.3K
Synthetic Biology
4.7K
Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...
Golden rice
Golden rice is a genetically modified...
4.7K
Protein 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
Conservation of Protein Domains Over Different Proteins
10.9K
Protein domains are small structurally independent units that are part of a single amino acid chain. Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
10.9K
Comparing Mitochondrial, Chloroplast, and Prokaryotic Genomes
12.5K
The present-day mitochondrial and chloroplast genomes have retained some of the characteristics of their ancestral prokaryotes and also have acquired new attributes during their evolution within eukaryotic cells. Like prokaryotic genomes, mitochondrial and chloroplast genomes neither bind with histone-like proteins nor show complex packaging into chromosome-like structures, as observed in eukaryotes. Unlike mitotic cell divisions observed in eukaryotic cells, mitochondria and chloroplasts...
12.5K
Genomics
36.3K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
36.3K


