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相关概念视频

Protein Networks02:26

Protein Networks

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An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
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Convolution Properties II01:17

Convolution Properties II

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The important convolution properties include width, area, differentiation, and integration properties.
The width property indicates that if the durations of input signals are T1 and T2, then the width of the output response equals the sum of both durations, irrespective of the shapes of the two functions. For instance, convolving two rectangular pulses with durations of 2 seconds and 1 second results in a function with a width of 3 seconds.
The area property asserts that the area under the...
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Chromatin Packaging02:21

Chromatin Packaging

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Each human somatic cell contains 6 billion base-pairs of DNA. Each base-pair is 0.34 nm long, which means that each diploid cell contains a staggering 2 meters of DNA. How is such a long DNA strand packed inside a nucleus measuring only 10 - 20 microns in diameter? 
The chromatin
In combination with specialized DNA binding protein called Histones, the DNA double helix forms a compact DNA: protein complex called chromatin. The chromatin itself is further compacted into higher-order...
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Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer...
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Inheritance of Chromatin Structures03:17

Inheritance of Chromatin Structures

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Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
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Convolution Properties I01:20

Convolution Properties I

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Convolution computations can be simplified by utilizing their inherent properties.
The commutative property reveals that the input and the impulse response of an LTI (Linear Time-Invariant) system can be interchanged without affecting the output:
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Investigation of Plant Interactions Across Common Mycorrhizal Networks Using Rotated Cores
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植物CTCIP:在植物中使用卷积神经网络和变压器进行染色体相互作用预测.

Zhenye Wang1,2, Siyu Zhou1,3,4, Ze Guo4

  • 1National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.

Plant biotechnology journal
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概括

使用深度学习的新型模型PlantCTCIP准确地预测了植物染色质相互作用. 该工具增强了对基因调节的理解,并通过识别目标基因和功能部位来帮助作物育种.

关键词:
TF协作合作TF协作合作染色素相互作用的作用.深度学习是一种深度学习.植物植物植物植物植物植物.监管要素 监管元素 监管元素

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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
  • 植物科学 植物科学

背景情况:

  • 染色体相互作用对于基因表达和表型特征至关重要,因为它通过将调节元素与向基因联系起来.
  • 预测这些相互作用是了解植物基因调节的关键.

研究的目的:

  • 开发和评估PlantCTCIP,这是一个用于预测植物染色素相互作用的深度学习模型.
  • 为玉米,大米,棉花和小麦构建全基因组染色体相互作用图.
  • 识别调节动机,转录因子及其影响色素相互作用的网络.

主要方法:

  • 在PlantCTCIP模型中利用了卷积神经网络和变压器架构.
  • 对四种植物物种进行了全基因组的染色质相互作用映射.
  • 使用Hi-C实验验并分析动机和转录因子丰富的验证预测.

主要成果:

  • 植物CTCIP显著提高了染色体相互作用预测准确度 (14.56%AUC用于近端促进体相互作用,9.6%用于远端促进体相互作用).
  • 确定了以eQTL和开放色素区域丰富的关键动机.
  • 分析了TF丰富和影响跨物种促进体相互作用的协同网络.

结论:

  • 植物CTCIP提供了一种先进的方法来预测植物染色体相互作用,有助于基因调节机制分析.
  • 该模型有助于识别远程调节元素和功能部位,支持作物育种和遗传改进.
  • 提供了对基因调节的新见解,并为各种作物提供智能育种策略.