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相关概念视频

Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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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...
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Master transcription regulators are regulatory proteins that are predominantly responsible for regulating the expression of multiple genes. Often these genes work in concert to drive a  complex process. Activation of a master transcription regulator can lead to a cascade of transcriptional activation necessary for that outcome. These regulators can directly bind to the regulatory sequences of the various genes involved, or they can indirectly regulate transcription by binding to regulatory...
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Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
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Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
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Updated: Jul 3, 2025

Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
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DeepRegFinder:基于深度学习的监管元素寻找器

Aarthi Ramakrishnan1, George Wangensteen2, Sarah Kim3

  • 1Friedman Brain Institute and Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.

Bioinformatics advances
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概括
此摘要是机器生成的。

DeepRegFinder是一个新的生物信息学工具,它使用机器学习以高精度识别DNA调节元素 (增强剂和促进剂). 它自动化数据处理,模型训练和预测,改进现有方法.

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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:

  • 包括增强剂和促进剂在内的DNA调节元件 (DREs) 对于控制基因表达至关重要.
  • 识别全基因组DREs对于理解基因调节至关重要.
  • 通过ChIP-seq检测到的基因组标记结合模式为DREs提供了独特的签名.

研究的目的:

  • 开发一个可定制和自动化的程序,DeepRegFinder,用于预测增强剂和促进剂.
  • 通过机器学习提高DRE识别的准确性和效率.
  • 为了使增强剂和促进剂能够被分类为活跃状态和平衡状态.

主要方法:

  • 利用卷积和循环神经网络进行模型训练和预测.
  • 开发了一个自动化数据处理,模型训练和预测DREs的管道.
  • 集成的组织蛋白标记 ChIP-seq 数据用于特征提取.

主要成果:

  • 与现有的增强器预测算法相比,DeepRegFinder表现出更好的精度和回忆.
  • 该工具成功地将增强剂和促进剂分为活跃状态和平衡状态.
  • 模块化管道简化和加速了DRE预测的应用.

结论:

  • DeepRegFinder提供了一种强大且易于使用的解决方案,用于基因组规模识别和描述DREs.
  • 自动化工作流程和先进的机器学习模型增强了对基因调节的研究.
  • 该工具提供了对各种细胞类型中活跃和平衡的调节元素的宝贵见解.