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相关概念视频

Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer is an enzyme that can...
Conservative Site-specific Recombination and Phase Variation02:53

Conservative Site-specific Recombination and Phase Variation

Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
The recognition sites for Cre recombinase called LoxP...
Transcription Attenuation in Prokaryotes02:42

Transcription Attenuation in Prokaryotes

Transcriptional attenuation occurs when RNA transcription is prematurely terminated due to the formation of a terminator mRNA hairpin structure.  Bacteria use these hairpins to regulate the transcription process and control the synthesis of several amino acids including histidine, lysine, threonine, and phenylalanine. Transcription attenuation takes place in the non-coding regions of mRNA.
There are several different mechanisms used to attenuate transcription. In ribosome mediated...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
DNA Microarrays02:34

DNA Microarrays

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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使用STew发现单细胞空间转录组的空间知情变异.

Nanxi Guo1,2, Juan Vargas2,3, Samantha Reynoso2,4

  • 1Biostatistics and Informatics PhD Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, United States.

Bioinformatics advances
|June 3, 2024
PubMed
概括

一种新的空间转录组方法STew集成了基因表达和空间数据,用于增强组织分析. 它可以在各种空间转录基因技术中准确识别细胞类型和疾病.

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科学领域:

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

背景情况:

  • 空间转录学 (ST) 技术为组织环境中的基因表达提供了洞察力.
  • 分析ST数据以整合空间信息与基因表达仍然是一个重大挑战.

研究的目的:

  • 介绍STew,一种可扩展的多视图表示学习方法,用于在ST中联合分析空间和基因表达数据.
  • 开发一个统计框架来评估模型适合ST数据分析.

主要方法:

  • STew使用多视图表示学习来共同分析空间和基因表达数据.
  • 一个数据驱动的统计框架被用来衡量模型合适度的好处.
  • 对人类和小鼠的ST数据进行了基准测试,并附有手册注释.

主要成果:

  • 与现有方法相比,STew在聚类精度和空间域连续性方面表现出卓越的表现.
  • 该方法对参数变化具有稳定性,适用于各种ST技术 (10× Visium,Slide-seqV2,10× Xenium).
  • 史蒂夫确定了空间知情的细胞类型集群,生物学上有意义的轴,以及牛皮的皮肤中的炎症性纤维细胞.

结论:

  • STew提供了一种可扩展和有效的方法来分析空间转录组数据.
  • 该方法准确地揭示了细胞类型分布和与疾病相关的空间.
  • STew的线性可扩展性确保了它对大规模ST数据集的实用性.