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相关概念视频

Cell Specific Gene Expression01:58

Cell Specific Gene Expression

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Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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The process of chromosome duplication during cell division requires genome-wide disruption and re-assembly of chromatin. The chromatin structure must be accurately inherited, reassembled, and maintained in the daughter cells to ensure lineage propagation.
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相关实验视频

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DeepDoublet识别了邻近的细胞依赖基因表达的基因表达.

Linbu Liao1, Junyoung Kim2, Kanghee Cho2

  • 1Cancer Institution, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

Genomics & informatics
|December 19, 2024
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概括
此摘要是机器生成的。

DeepDoublet是一种新的深度学习工具,可以分解物理相互作用的细胞转录组. 它揭示了细胞特异性基因表达,如肝细胞中的Angptl3与肝脏内皮细胞相互作用,推进了细胞与细胞相互作用研究.

关键词:
细胞细胞相互作用深度学习是一种深度学习.双重分解是一种双重分解.单细胞RNA测序的一个细胞.

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科学领域:

  • 细胞生物学 细胞生物学
  • 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:

  • 细胞与细胞之间的相互作用对于组织功能和恒常性至关重要.
  • 单细胞RNA测序 (scRNAseq) 传统上通过连接体-受体共同表达来推断相互作用.
  • 最近的进展允许物理相互作用细胞的RNA测序,使相互作用研究没有共同表达假设.

研究的目的:

  • 介绍DeepDoublet,这是一个深度学习工具,用于解物理相互作用的细胞对 (doublets) 的转录组.
  • 为了能够研究特定于相互作用细胞类型的基因表达.
  • 为了识别新的细胞邻居依赖的基因表达模式.

主要方法:

  • 开发DeepDoublet,这是一种深度学习算法,旨在将两种物理交互的细胞中的转录组数据分开.
  • 应用DeepDoublet来分析由肝细胞和肝脏内皮细胞 (LEC) 形成的双倍细胞.
  • 验证DeepDoublet能够准确地将双重转录组分解为单个细胞类型配置文件的能力.

主要成果:

  • DeepDoublet成功地将肝细胞-LEC双体的转录组分解成不同的肝细胞和LEC配置文件.
  • 该工具在与LEC相互作用时,在肝细胞中确定了特定的基因表达模式.
  • 值得注意的是,参与血管形成的基因 - - 血管类3 (Angptl3) 被确定为在相互作用的肝细胞中特别表达.

结论:

  • DeepDoublet提供了一种新的计算方法来分析物理相互作用细胞的转录组.
  • 该工具有助于发现细胞邻居依赖的基因表达.
  • 这些发现突显了DeepDoublet在发现细胞与细胞相互作用期间特定环境的基因调节方面的潜力.