细胞类型在物种之间匹配,使用蛋白质嵌入和转移学习
Kirti Biharie1,2,3, Lieke Michielsen1,2,3, Marcel J T Reinders1,2,3
1Delft Bioinformatics Lab, Delft University of Technology, Delft 2628XE, The Netherlands.
Bioinformatics (Oxford, England)
|June 30, 2023
概括
我们开发了TACTiCS,这是一种新型模型,可以使用基因序列信息对各个物种的细胞类型进行对齐. 这种方法可以准确地将细胞类型标签从物种转移到物种之间,从而改善跨物种研究.
科学领域:
- 进行比较的基因组学.
- 生物信息学是一种生物信息学.
- 单细胞RNA测序分析分析
背景情况:
- 将实验结果翻译成像老鼠和人类这样的物种之间的转换是至关重要的,但由于生物差异而具有挑战性.
- 当前的方法往往忽略进化基因信息,仅专注于一对一的正义基因,限制跨物种细胞类型的对齐.
研究的目的:
- 介绍TACTiCS (跨物种分析中转移和对齐细胞类型),一种用于跨物种准确的细胞类型匹配和对齐的新模型.
- 利用全面的基因进化信息来改善跨物种比较分析.
主要方法:
- TACTiCS利用自然语言处理模型根据蛋白质序列匹配基因.
- 神经网络在物种内分类细胞类型,然后进行转移学习以在物种之间传播标签.
- 该模型被应用于来自人类,小鼠和海的初级运动皮质的单细胞RNA测序 (scRNA-seq) 数据.
主要成果:
- TACTiCS成功匹配和对齐了人类,老鼠和海小鼠scRNA-seq数据集中的细胞类型.
- 该模型在与Seurat和SAMap等既定方法相比显示出更高的性能.
- TACTiCS的基因匹配方法,利用蛋白质序列,产生了比BLAST更准确的细胞类型对应.
结论:
- TACTiCS为跨物种细胞类型对齐提供了强大的框架,增强了生物研究的翻译潜力.
- 该模型利用更广泛的进化基因信息的能力克服了以前方法的局限性.
- TACTiCS在比较单细胞转录组学方面取得了重大进展,并提供公开可用的代码和数据.
相关概念视频
02:18Types of Genetic Transfer Between Organisms
5.4K
5.4K
02:26Conservation 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
02:26Conservation of Protein Domains
3.1K
3.1K
02:51Multi-species Conserved Sequences
4.0K
Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
4.0K
02:07Improving Translational Accuracy
11.7K
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...
11.7K
01:24Tissue Transplantation
415
Tissue transplantation is a significant medical procedure involving the transfer of cells, tissues, or organs from a donor to a recipient, with the primary aim of restoring lost functions. This procedure is crucial in treating a broad spectrum of diseases, including kidney diseases, liver failure, heart disease, and certain types of cancers.
The Biology of Tissue Transplantation
The biology of tissue transplantation hinges on the Major Histocompatibility Complex (MHC) molecules. These molecules...
The Biology of Tissue Transplantation
The biology of tissue transplantation hinges on the Major Histocompatibility Complex (MHC) molecules. These molecules...
415