将基因表达水平与转录因子结合部位相关联,有助于从转录组数据中识别关键的转录因子
Tinghua Huang1, Siqi Niu1, Fanghong Zhang1
1College of Animal Science and Technology, Yangtze University, Jingzhou, China.
Frontiers in genetics
|December 16, 2024
概括
这项研究引入了分析转录组数据的改进方法,通过将基因表达与结合部位相关联来识别关键的转录因子. 表达式差分 (ED) 方法和混合密度曲线权重证明最有效,确定了644名候选人.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 基因组学就是基因组学.
背景情况:
- 准确识别转录因子 (TFs) 对于从转录组数据中理解基因调节至关重要.
- 使用过基因表达和TF结合位相关的传统方法可能会产生虚假的结果.
- 开发强大的分析方法对于可靠的TF发现至关重要.
研究的目的:
- 评估和优化将基因表达与TF结合部位相关联的方法,以改进TF识别.
- 解决当前相关性分析的局限性,例如无法检测负相关性.
- 从大规模的转录组数据集中确定关键的转录因子.
主要方法:
- 他们比较了生成排列基因表达列表的四种方法:恒星坐标地图转换 (START),表达差分数 (ED),偏好表达量 (PEM) 和特异性量 (SPM).
- 肯德尔的相关性使用五种权衡方法来应用:标准 (STD),线性,混合线性,密度曲线和混合密度曲线.
- 对来自1,206个细胞系的转录组数据进行了分析.
主要成果:
- 表达差异得分 (ED) 被确定为创建排名基因列表的最佳方法,有效处理负相关性.
- 混合密度曲线权重方法在识别TF方面表现出最高的灵敏度.
- 总共有644个转录因子候选物被确定,其中六个随后通过湿实验室实验验验证.
结论:
- 结合ED方法和MIXED-DENSITY-CURVE权重,提供了一种可靠的方法,用于从转录组数据中识别关键转录因子.
- 这种优化的方法提高了生物信息学TF发现的准确性和可靠性.
- 有Jinzer和Flaver软件包可用于实现这些先进的分析技术.
更多相关视频
12:29Identifying Transcription Factor Olig2 Genomic Binding Sites in Acutely Purified PDGFRα+ Cells by Low-cell Chromatin Immunoprecipitation Sequencing Analysis
Published on: April 16, 2018
9.2K
07:23Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
Published on: June 15, 2016
8.4K
相关概念视频
Transcription Factors
75.6K
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...
75.6K
General Transcription Factors
5.2K
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...
5.2K
Cooperative Binding of Transcription Regulators
2.0K
2.0K
RNA Polymerase II Accessory Proteins
9.1K
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...
9.1K
Co-activators and Co-repressors
7.3K
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...
7.3K
Master Transcription Regulators
6.9K
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...
6.9K
