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相关概念视频

Cell Specific Gene Expression01:58

Cell Specific Gene Expression

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...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

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...
Cell Specific Gene Expression01:58

Cell Specific Gene Expression

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...
Regulation of Expression Occurs at Multiple Steps02:24

Regulation of Expression Occurs at Multiple Steps

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...
Structure of a Gene01:30

Structure of a Gene

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...
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

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 addition of a...

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相关实验视频

Updated: Jun 26, 2026

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
10:12

Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

Published on: January 10, 2019

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通过可解释的深度学习推断单细胞空间基因表达与组织形态.

Yue Zhao, Elaheh Alizadeh, Yang Liu

    bioRxiv : the preprint server for biology
    |June 25, 2024
    PubMed
    概括

    我们开发了SPiRiT,一种视觉转换器框架,用于从组织图像中预测空间基因表达. 这种方法使用组织学准确推断细胞基因活性,推进空间转录和诊断.

    科学领域:

    • 计算生物学 计算生物学
    • 基因组学就是基因组学.
    • 生物技术是生物技术.

    背景情况:

    • 细胞的空间布局对于发育和器官生成至关重要.
    • 使用空间奥米克数据的深度学习揭示了复杂的生物模式和疾病洞察力.
    • 组织学图像和计算方法分析细胞异质性和空间数据.

    研究的目的:

    • 开发一个视觉转换器 (ViT) 框架,SPiRiT,用于将组织学特征映射到空间单细胞转录学特征.
    • 通过对超参数调整进行交叉验证和模型解释来增强框架.
    • 从人类和小鼠模型中的基因病理图像预测单细胞空间基因表达.

    主要方法:

    • 开发了SPiRiT,一个视觉转换器 (ViT) 框架,集成交叉验证和模型解释.
    • 应用 SPiRiT 来预测来自 H&E 染色组织学图像的空间基因表达.
    • 使用Xenium和Visium (10x Genomics) 数据集对人类乳腺癌和整个小鼠幼进行了SPiRiT评估.

    主要成果:

    • 从组织形态学上,SPiRiT可以准确地预测单细胞的空间基因表达.
    • 模型解释确定了与特定细胞类型和标记基因 (FASN,POSTN,IL7R) 相关的高分辨率,高注意力区域 (HAR).

    更多相关视频

    Mapping the Emergent Spatial Organization of Mammalian Cells using Micropatterns and Quantitative Imaging
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    Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
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    Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

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    相关实验视频

    Last Updated: Jun 26, 2026

    Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues
    10:12

    Droplet Barcoding-Based Single Cell Transcriptomics of Adult Mammalian Tissues

    Published on: January 10, 2019

    18.5K
    Mapping the Emergent Spatial Organization of Mammalian Cells using Micropatterns and Quantitative Imaging
    09:56

    Mapping the Emergent Spatial Organization of Mammalian Cells using Micropatterns and Quantitative Imaging

    Published on: April 30, 2019

    6.6K
    Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection
    09:19

    Spatial Profiling of Protein and RNA Expression in Tissue: An Approach to Fine-Tune Virtual Microdissection

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  • 与ST-Net相比,SPiRiT在预测准确度上有40%的改进,预测基因表达和瘤区域注释之间具有很高的一致性.
  • 结论:

    • SPiRiT能够从多种物种和器官的组织形态学推断空间单细胞基因表达.
    • 该框架的模型解释和ViT的整合为空间转录学提供了一个通用的工具.
    • 这种方法加速了科学发现,提高了医学诊断和治疗的精度.