从单细胞转录组中计算出超过2500个表面蛋白质的丰富性,并与文本无关的零射击深层合奏进行了相关分析
Ruoqiao Chen1, Jiayu Zhou2, Bin Chen3
1Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI 48824, USA.
Cell systems
|September 7, 2024
概括
新的深度学习模型SPIDER能够从基因表达数据中准确预测细胞表面蛋白质水平. 这种方法为癌症研究和药物发现中的大规模应用提供了更好的概括性.
科学领域:
- 单细胞基因组学 单细胞基因组学
- 计算生物学是一种计算生物学.
- 蛋白质组学是指蛋白质组学.
背景情况:
- 细胞表面蛋白对于药物向和识别细胞类型至关重要.
- 同时测量RNA和蛋白质是可能的,如CITE-seq.
- 现有的用于蛋白质预测的机器学习模型在不同的生物环境中存在规模和概括性的限制.
研究的目的:
- 从单细胞RNA测序数据开发一种新的计算模型,以准确和可扩展地预测单细胞表面蛋白质的丰富性.
- 创建一个文本无关的模型,可以在各种生物样本和疾病状态中很好地概括.
- 为了使表面蛋白质的大规模预测用于下游生物分析.
主要方法:
- 开发SPIDER (使用单细胞RNA测序的深层组合进行表面蛋白质预测),这是一个无背景的零射击深层组合模型.
- 培训和比较SPIDER与现有最先进的方法,使用已公布的CITE-seq数据集.
- 应用SPIDER来预测来自单细胞转录组的2500多种表面蛋白质的丰富性.
主要成果:
- 与其他最先进的方法相比,SPIDER在综合基准测试中表现出更高的性能.
- 该模型实现了对表面蛋白质丰富性的准确,大规模预测.
- 蜘蛛在各种生物环境中表现出强大的概括能力.
结论:
- 蜘蛛提供了一种强大而通用的工具,用于从转录基因数据中预测细胞表面蛋白质表达.
- 该模型的预测促进了诸如细胞类型注释,生物标志物发现和癌症细胞相互作用分析等应用.
- 蜘蛛增强了单细胞RNA测序数据的实用性,用于生物发现和治疗标识.
关键词:
在CITE-seqq.结肠直肠癌是什么意思肝细胞癌是肝细胞癌.免疫疗法 免疫疗法机器学习是机器学习.蛋白质组学 蛋白质组学这就是 scRNA-seqq.单细胞的奥米克.表面蛋白质是一种表面蛋白质.零射击学习的学习更多相关视频
相关概念视频
03:21RNA-seq
9.9K
RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
9.9K
02:24Ribosome Profiling
3.5K
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...
3.5K