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相关概念视频

Multi-species Conserved Sequences02:51

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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved...
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Evolutionary Relationships through Genome Comparisons02:54

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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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相关实验视频

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SEdb 3.0:一个跨多个物种的全面超级增强器数据库.

Shuang Song1,2, Liyuan Liu1,2, Chenchen Feng3

  • 1The First Affiliated Hospital and Hunan Provincial Key Laboratory of Multi-omics and Artificial Intelligence of Cardiovascular Diseases, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.

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概括

超级增强剂 (SE) 对细胞身份至关重要. SEdb 3.0 扩展了这一资源,在物种中增加了数百万个SE,添加增强器RNA和辅因子结合点,以获得更深入的生物学见解.

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科学领域:

  • 基因组学就是基因组学.
  • 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
  • 生物信息学是一种生物信息学.

背景情况:

  • 超级增强剂 (SE) 是关键的控制细胞特异性基因表达和身份的 cis 调控元素.
  • 现有的数据库提供有限的SE信息,阻碍了跨不同物种和监管机制的全面分析.

研究的目的:

  • 介绍SEdb 3.0,这是对SE及其监管注释的大幅扩展和更新的资源.
  • 增强SEDb的规模和实用性,用于人类,模型生物和植物的研究.
  • 为深入研究SE函数提供新的功能注释和分析工具.

主要方法:

  • 从5387个H3K27ac ChIP-seq样本中精选了3,478,186个SE,这些样本来自四种物种 (人类,老鼠,阿拉比多普西斯塔利亚纳,玉米).
  • 整合了各种各样的表观遗传特征:增强子RNA (eRNA),转录辅因子 (TcoF) 结合部位和染色体调节器 (CRs).
  • 扩展了现有的注释,包括转录因子 (TF) ChIP-seq数据,TF动机和SE相关的eQTL基因调控对.

主要成果:

  • SEdb 3.0为人类和老鼠的SE条目提供了两倍的扩展,并引入了植物SE数据.
  • 新的注释提供了对SE转录活性 (eRNA),调节机制 (TcoF结合) 和染色质状态 (CRs) 的见解.
  • 在TF ChIP-seq数据,TF动机和eQTL关联中大幅增加,以及新的基因-SE关联推断策略和分析工具.

结论:

  • SEdb 3.0代表着一个重大的升级,为SE研究提供了一个全面和用户友好的平台.
  • 扩展的数据集和增强的注释方便了对SE生物学意义和监管作用的详细调查.
  • 这种资源显著推进了动物和植物王国中SEs的研究.