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相关概念视频

Cooperative Binding of Transcription Regulators02:13

Cooperative Binding of Transcription Regulators

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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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Transcription Factors02:16

Transcription Factors

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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...
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Conserved Binding Sites01:49

Conserved Binding Sites

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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
General Transcription Factors01:30

General Transcription Factors

5.3K
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...
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Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

11.1K
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...
11.1K
Combinatorial Gene Control02:33

Combinatorial Gene Control

8.3K
Combinatorial gene control is the synergistic action of several transcriptional factors to regulate the expression of a single gene. The absence of one or more of these factors may lead to a significant difference in the level of gene expression or repression.
The expression of more than 30,000 genes is controlled by approximately 2000-3000 transcription factors. This is possible because a single transcription factor can recognize more than one regulatory sequence. The specificity in gene...
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相关实验视频

Updated: Jun 26, 2025

Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation

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多TFBS:一个具有多通道的时空网络,用于预测转录因子结合站点.

Jujuan Zhuang1, Xinru Huang1, Shuhan Liu1

  • 1The School of Science, Dalian Maritime University, Dalian 116026, China.

Journal of chemical information and modeling
|May 11, 2024
PubMed
概括
此摘要是机器生成的。

本研究介绍了MulTFBS,这是一个新的深度学习框架,用于预测转录因子结合位点 (TFBS). 多TFBS集成了多种DNA序列特征,在回归和分类任务中表现优于现有方法.

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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins

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Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
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Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences

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相关实验视频

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Real-time Analysis of Transcription Factor Binding, Transcription, Translation, and Turnover to Display Global Events During Cellular Activation
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PAR-CliP - A Method to Identify Transcriptome-wide the Binding Sites of RNA Binding Proteins
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Enhanced Yeast One-hybrid Screens To Identify Transcription Factor Binding To Human DNA Sequences
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科学领域:

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

背景情况:

  • 了解转录因子结合特异性对于基因调节至关重要.
  • 以前用于预测转录因子结合位点 (TFBS) 的方法主要使用DNA结构和一热编码.
  • 对于TFBS预测,自然语言处理技术 (如词嵌入) 尚未得到充分探索.

研究的目的:

  • 开发一个先进的计算框架来预测TFBSs.
  • 整合多种类型的DNA序列特征,以提高预测准确度.
  • 为了利用深度学习,包括自然语言处理概念,用于TFBS预测.

主要方法:

  • 开发了一个多道深度学习框架,MulTFBS.
  • 将一热编码,文字嵌入编码和3D DNA结构特征集成到单独的道中.
  • 采用一个时空网络,结合CNN,双向LSTM和用于特征提取的注意力机制.

主要成果:

  • 与六种最先进的方法相比,MulTFBS在66个通用蛋白结合微阵列数据集上表现出卓越的性能.
  • 在回归任务中获得了0.698的平均R2和0.833的平均PCC,超过了次优CRPTS方法.
  • 在使用TF ChIP-seq数据的TFBS分类任务中表现出色.

结论:

  • 多TFBS框架有效地整合了各种DNA序列特征,以准确预测TFBS.
  • 拟议的深度学习架构成功地捕获了高层次序列信息.
  • 多TFBS代表了计算TFBS预测在回归和分类方面取得的重大进展.