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相关概念视频

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

9.9K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
9.9K
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

6.4K
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome.  Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
6.4K
Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

914
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...
914
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

5.7K
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...
5.7K
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

7.1K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
7.1K
Conserved Binding Sites01:49

Conserved Binding Sites

4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.2K

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相关实验视频

Updated: Jul 6, 2025

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

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使用EUGENe对调节序列的预测分析.

Adam Klie1,2, David Laub1,2, James V Talwar1,2

  • 1Department of Medicine, University of California San Diego, La Jolla, CA, USA.

Nature computational science
|January 4, 2024
PubMed
概括

我们开发了EUGENe,这是一个用于监管基因组学深度学习的FAIR工具包. 该软件简化了基因组序列分析,使深度学习应用程序更易于访问和可重复使用.

更多相关视频

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
11:35

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

Published on: August 21, 2016

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相关实验视频

Last Updated: Jul 6, 2025

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes
07:55

Using SCOPE to Identify Potential Regulatory Motifs in Coregulated Genes

Published on: May 31, 2011

10.4K
Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
11:34

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins

Published on: August 9, 2019

6.7K
Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA
11:35

Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

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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
  • 生物信息学是一种生物信息学.

背景情况:

  • 深度学习越来越多地用于研究 cis-regulatory 功能.
  • 在监管基因组学中,现有的深度学习软件往往缺乏FAIR (可查找,可访问,可互操作,可重复使用) 原则.
  • 需要强大的,用户友好的工具来促进基因组学中的深度学习分析.

研究的目的:

  • 推出EUGENe,一个旨在深度学习基因组序列分析的FAIR工具包.
  • 为基因组学中端到端的深度学习工作流提供灵活和可扩展的平台.
  • 通过实际应用来证明EUGENe的实用性.

主要方法:

  • 欧基因包括数据处理 (提取,转换,加载),模型实现 (实例化,培训各种架构) 和分析 (评估,解释) 的模块.
  • 该工具包支持各种常见的基因组文件格式.
  • 它被应用于基因组学中的三个不同的预测建模任务.

主要成果:

  • 欧基因成功地促进了基因组序列数据的提取,转换和加载.
  • 该工具包允许实例化,初始化和训练各种深度学习模型架构.
  • EUGENE有助于评估和解释受过训练的模型的行为,证明其在预测基因组学中的实用性.

结论:

  • 欧基因是一个符合FAIR标准的工具包,它解决了监管基因组学当前深度学习软件的局限性.
  • 该工具包提供了一个精简,灵活和可扩展的界面,用于深度学习序列分析.
  • 欧基因旨在促进深度学习应用在基因组学研究中的协作生态系统.