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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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Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

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The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
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Overview of Cell-Matrix Interactions01:24

Overview of Cell-Matrix Interactions

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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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Combinatorial Gene Control02:33

Combinatorial Gene Control

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Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
8.3K
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

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Gene expression can be regulated at almost every step from gene to protein. Transcription is the step that is most commonly regulated. This involves the binding of proteins to short regulatory sequences on the DNA. This association can either promote or inhibit the transcription of a gene associated with the respective sequence.
Transcription results in the generation of precursor (pre-mRNA) that consists of both exons and introns, which needs further processing before being translated to a...
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Structure of a Gene01:30

Structure of a Gene

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A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
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相关实验视频

Updated: Jun 5, 2025

Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers
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Author Spotlight: Impact of Intergenic Interactions on Disease-Identifying Dark Biomarkers

Published on: March 1, 2024

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iMIRACLE:一个代的多视图图神经网络,以从空间转录基因数据模型细胞间基因调节.

Ziheng Duan1, Siwei Xu1, Cheyu Lee1

  • 1University of California, Irvine, Irvine, CA, USA.

Proceedings of the ... ACM International Conference on Information & Knowledge Management. ACM International Conference on Information and Knowledge Management
|December 16, 2024
PubMed
概括
此摘要是机器生成的。

一个新的图形神经网络iMiracle通过整合基因表达和连接体-受体相互作用来解码细胞-细胞通信. 这种方法改善了空间转录学分析,以了解细胞间调节.

关键词:
细胞细胞通讯 细胞细胞通讯图形神经网络的神经网络细胞间基因调节 细胞间基因调节空间转录学 空间转录学

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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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Author Spotlight: An Integrated Workflow to Study the Promoter-Centric Spatio-Temporal Genome Architecture in Scarce Cell Populations
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Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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科学领域:

  • 基因组学就是基因组学.
  • 计算生物学 计算生物学
  • 系统生物学 系统生物学

背景情况:

  • 空间转录学使细胞微环境中的基因表达分析成为可能.
  • 通过连接体-受体 (LR) 相互作用的细胞-细胞通信 (CCC) 驱动细胞反应.
  • 现有的方法缺乏强大的方法来将CCC与基因表达变化联系起来,以获得生物学见解.

研究的目的:

  • 开发一种用于建模细胞间调节的新型计算方法.
  • 将空间转录学数据与细胞间通信网络相结合.
  • 推断由LR相互作用驱动的细胞特异性基因调控得分.

主要方法:

  • 开发了iMiracle,一个代的多视图图形神经网络.
  • 集成的细胞间和细胞内网络用于基因表达估计.
  • 采用代学习来解决CCC网络中的数据稀疏性.
  • 使用LR对贡献推断的细胞特异性联体基因调控得分.

主要成果:

  • iMiracle 在不同数据集的基因表达赋值中表现出卓越的性能.
  • 该方法在推断监管得分方面表现优于现有的方法.
  • 评估了来自三个平台的九个模拟和八个真实空间转录组数据集.

结论:

  • 通过整合基因表达和CCC数据,iMiracle有效地建模细胞间调节.
  • 该工具通过提供细胞特异性监管洞察力,提高了空间转录学的解释性.
  • iMiracle是一款开源软件,旨在促进细胞间通信和转录调节的研究.