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相关概念视频

Transcription Factors02:16

Transcription Factors

75.5K
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
75.5K
Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

6.3K
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...
6.3K
Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

11.0K
Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
11.0K
General Transcription Factors01:30

General Transcription Factors

5.1K
Tissue-specific transcription factors contribute to diverse cellular functions in mammals. For example, the gene for beta globin, a major component of hemoglobin, is present in all cells of the body. However, it is only expressed in red blood cells because the transcription factors that can bind to the promoter sequences of the beta globin gene are only expressed in these cells. Tissue-specific transcription factors also ensure that mutations in these factors may impair only the function of...
5.1K
Master Transcription Regulators02:23

Master Transcription Regulators

6.8K
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...
6.8K
Conserved Binding Sites01:49

Conserved Binding Sites

4.1K
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...
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相关实验视频

Updated: May 23, 2025

High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy
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High Sensitivity Measurement of Transcription Factor-DNA Binding Affinities by Competitive Titration Using Fluorescence Microscopy

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SNPeBoT:用于预测转录因子等位基因特定结合的工具.

Patrick Gohl1, Baldo Oliva2

  • 1Department of Medicine and Life Sciences, SBI-GRIB, Universitat Pompeu Fabra, 08003, Barcelona, Catalonia, Spain.

BMC bioinformatics
|March 11, 2025
PubMed
概括
此摘要是机器生成的。

我们开发了SNPeBoT,这是一种深度学习模型,可以准确预测单核酸多态 (SNP) 如何影响转录因子结合. 这种工具可以更好地发现致病的非编码突变.

关键词:
基因调节 基因调节神经网络的神经网络转录因子是一种转录因子.

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Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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相关实验视频

Last Updated: May 23, 2025

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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:

  • 非编码DNA中的突变可以破坏转录因子的结合,可能导致疾病.
  • 了解转录因子结合模式和遗传变异的影响至关重要,但有限.
  • 深度学习提供了一个有前途的方法来建模这些复杂的相互作用.

研究的目的:

  • 开发一种深度学习模型,用于预测单核酸多态 (SNP) 对转录因子结合的影响.
  • 提高预测等位基特定结合 (ASB) 事件的准确性和回忆.
  • 为识别与疾病相关的非编码突变提供一种工具.

主要方法:

  • 训练了一个卷积神经网络 (CNN),使用来自ChIP-seq的基因特异结合 (ASB) 数据和来自蛋白结合微阵列 (PBM) 的DNA结合域数据.
  • 衍生出的E-score资料用于与ASB事件相关的参考和替代DNA序列.
  • 利用了来自113个转录因子的18211个E-score配置文件,分为培训,验证和测试数据集.

主要成果:

  • 与现有的基准预测平台相比,开发的CNN模型显示出更高的准确性和ASB回忆力.
  • 该模型有效地预测SNP是否导致转录因子结合的增加,损失或无变化.
  • 对SNP效应预测的既定工具进行了性能验证.

结论:

  • 引入了SNPeBoT (单核酸多态化对转录因子结合的影响),可作为独立工具和Web服务器.
  • 增强的预测准确度和ASB事件的恢复可以帮助发现疾病相关的非编码突变.
  • SNPeBoT为遗传研究和疾病关联研究提供了宝贵的资源.