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相关概念视频

Contact-dependent Signaling01:19

Contact-dependent Signaling

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Contact-dependent signaling, as the name suggests, requires that communicating cells be in direct contact with each other. This is achieved either through receptor-ligand interactions or by specialized cytoplasmic channels that allow the flow of small molecules between cells. In animal cells, channels called gap junctions facilitate contact-dependent signaling in certain tissues, whereas, plasmodesmata perform a similar function in plants.
Gap Junctions
In animal cells, gap junctions are formed...
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What is Cell Signaling?02:03

What is Cell Signaling?

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Despite the protective membrane that separates a cell from the environment, cells need the ability to detect and respond to environmental changes. Additionally, cells often need to communicate with one another. Unicellular and multicellular organisms use a variety of cell signaling mechanisms to communicate to respond to the environment.
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Gap Junctions01:37

Gap Junctions

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Multicellular organisms employ a variety of ways for cells to communicate with each other. Gap junctions are specialized proteins that form pores between neighboring cells in animals, connecting the cytoplasm between the two, and allowing for the exchange of molecules and ions. They are found in a wide range of invertebrate and vertebrate species, mediate numerous functions including cell differentiation and development, and are associated with numerous human diseases, including cardiac and...
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Membrane lipids such as phosphatidylinositol (PI) are precursors for several membrane-bound and soluble second messengers. Specific kinases phosphorylate PI and produce phosphorylated inositol phospholipids. One such inositol phospholipids are the  phosphatidylinositol-4,5 bisphosphate [PI(4,5)P2], present in the inner half of the lipid bilayer. Upon ligand binding, GPCR stimulates Gq proteins to turn on phospholipase Cꞵ. Activated phospholipase Cꞵ cleaves PI(4,5)P2 and...
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The extracellular matrix or ECM holds cells together to form a tissue and allows the cells within the tissue to communicate. ECM comprises proteins such as fibronectin, collagen, laminin, etc. The most abundant protein in this space is collagen. Collagen fibers are interwoven with carbohydrate-containing protein molecules called proteoglycans. ECM allows cell migration and provides a structural scaffold at cell adhesion that anchors the cell when the extracellular matrix proteins interact with...
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相关实验视频

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A Versatile Automated Platform for Micro-scale Cell Stimulation Experiments
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细胞GAT:一个基于GAT的方法来构建一个细胞通信网络,集成多态信息.

Tianjiao Zhang1, Zhenao Wu1, Liangyu Li1

  • 1College of Computer and Control Engineering, Northeast Forestry University, Harbin 150040, China.

Biomolecules
|March 28, 2025
PubMed
概括
此摘要是机器生成的。

通过将蛋白质-蛋白质相互作用与基因表达数据集成,CellGAT增强了细胞通信网络预测. 这种新的框架准确地推断出细胞间通信,影响下游通路和药物干预.

关键词:
细胞细胞相互作用深度学习是一种深度学习.图表注意力网络的图表.图表卷积神经网络 卷积神经网络这就是scRNA-seqq.

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相关实验视频

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科学领域:

  • 计算生物学 计算生物学
  • 系统生物学 系统生物学
  • 生物信息学是一种生物信息学.

背景情况:

  • 细胞间通信通过细胞间信号来协调多细胞生物的发展.
  • 推断细胞通信的现有计算方法往往忽略了蛋白质-蛋白质相互作用 (PPI),这可能会限制准确性.

研究的目的:

  • 开发一种新的计算框架,CellGAT,用于准确推断细胞间通信网络.
  • 整合多样化的生物数据,包括基因表达和PPI,进行强大的细胞通信分析.

主要方法:

  • 细胞GAT集成了基因表达,PPI,蛋白质复合体和通路信息.
  • 它在单细胞RNA测序 (scRNA-seq) 数据上使用节点嵌入和图表注意网络.
  • 一个内置的细胞聚类算法用于全面分析.

主要成果:

  • 通过利用PPI证据,CellGAT准确地预测了细胞-细胞通信 (CCC).
  • 该框架有效地分析了CCC对下游途径和邻近细胞的影响.
  • 在分析与药物干预相关的效果方面,CellGAT证明了它的实用性.

结论:

  • 细胞GAT为推断细胞通信网络提供了一种强大,综合的方法.
  • 该框架将PPI纳入框架的能力提高了预测准确性,特别是在没有先前的细胞类型信息的情况下.
  • 细胞GAT为细胞协调和潜在的治疗策略提供了宝贵的见解.