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Cell Specific Gene Expression01:58

Cell Specific Gene Expression

13.9K
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...
13.9K
Heterochromatin02:38

Heterochromatin

14.6K
The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at...
14.6K
cAMP-dependent Protein Kinase Pathways01:25

cAMP-dependent Protein Kinase Pathways

6.6K
Cyclic Adenosine Monophosphate (cAMP) is an essential second messenger that activates protein kinase A (PKA) and regulates various biological processes. A single epinephrine molecule binds to GPCR and activates several heterotrimeric G proteins, each stimulating multiple adenylyl cyclase, amplifying the signal, and synthesizing large numbers of cAMP molecules. Small changes in cAMP concentration affect PKA activity. The binding of four cAMP molecules induces a conformational change in PKA,...
6.6K
IP3/DAG Signaling Pathway01:11

IP3/DAG Signaling Pathway

12.4K
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...
12.4K
GPCRs Regulate Adenylyl Cylase Activity01:09

GPCRs Regulate Adenylyl Cylase Activity

5.9K
Some GPCRs transmit signals through adenylyl cyclase (AC), a transmembrane enzyme. AC helps synthesize second messenger cyclic adenosine monophosphate (cAMP). AC catalyzes cyclization reaction and converts ATP to cAMP by releasing a pyrophosphate. The pyrophosphate is further hydrolyzed to phosphate by the enzyme pyrophosphatase, which drives cAMP synthesis to completion. However, cAMP is rapidly degraded to 5′ AMP by the enzymes phosphodiesterase (PDE), preventing overstimulation of...
5.9K
Cell Lines01:16

Cell Lines

8.2K
A cell line is a population of cells grown in vitro that can be subcultured over several generations. Normal cells cease to divide after a certain number of cell divisions, a process known as replicative senescence. This number, called the Hayflick limit, was conceptualized by Leonard Hayflick in 1961 when he observed that fetal cells grown in culture could only divide 40-60 times. This limit is due to the shortening of the telomeres during each round of cell division, preventing cell division...
8.2K

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相关实验视频

Updated: Sep 13, 2025

Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information
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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

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PuMA:PubMed基因/细胞类型关系图谱

Lucas Bickmann1, Sarah Sandmann1, Carolin Walter2

  • 1Institute of Medical Data Science, Otto-von-Guericke University Magdeburg, Magdeburg, Germany.

BMC bioinformatics
|July 30, 2025
PubMed
概括

这项研究介绍了PubMed基因/细胞类型关系图谱 (PuMA),这是一个基于文献的细胞类型注释工具. PuMA从PubMed中提取基因和细胞类型信息,帮助研究人员自动识别细胞类型.

关键词:
细胞类型的注释.数据库数据库数据库是一个数据库.机器学习是机器学习.自然语言处理自然语言处理.在PubMed上发现了这一点.

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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq

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Using In Vivo and Tissue and Cell Explant Approaches to Study the Morphogenesis and Pathogenesis of the Embryonic and Perinatal Aorta
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Using In Vivo and Tissue and Cell Explant Approaches to Study the Morphogenesis and Pathogenesis of the Embryonic and Perinatal Aorta

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相关实验视频

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Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information

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Multiplexed Analysis of Retinal Gene Expression and Chromatin Accessibility Using scRNA-Seq and scATAC-Seq
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科学领域:

  • 生物信息学是一种生物信息学.
  • 计算生物学 计算生物学
  • 基因组学就是基因组学.

背景情况:

  • 自动化的细胞类型注释对于单细胞分析至关重要.
  • 现有的工具依赖于精心策划的数据库或机器学习,但不充分探索将文献知识纳入.

研究的目的:

  • 使用PubMed.开发一种基于文献的细胞类型注释工具.
  • 为了促进从科学文献中提取和可视化基因细胞类型关系.

主要方法:

  • 开发了PubMed基因/细胞类型关系图谱 (PuMA) 带有网页界面.
  • 利用基于机器学习的命名实体识别模型从PubMed中提取基因和细胞类型概念.
  • 链接生物医学本体学,并开发了基因细胞类型关系的排名得分.

主要成果:

  • PuMA提供了一个可搜索的界面,具有交互式图形可视化,用于探索基因-细胞类型关系.
  • 结果可以追溯到特定的PubMed文章.
  • 在鼠标和人类数据集中,PuMA 展示了与手动策划的数据库相比的竞争性性能.

结论:

  • PuMA允许使用PubMed文章进行自动化的细胞类型注释,补充现有数据库.
  • 该软件框架支持通过定期的物品进口增加知识更新.
  • 基于最新的科学文献,PuMA为研究人员提供了一种有价值的工具,用于分析和自动化细胞类型注释.