CoVar:一种可概括的机器学习方法,用于识别驱动变异基因表达的协调调节者
Satyaki Roy1, Shehzad Z Sheikh2, Terrence S Furey3
1Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, United States of America.
PLoS computational biology
|April 17, 2024
概括
CoVar是一种机器学习 (ML) 框架,通过分析基因表达网络相互作用的变化来识别关键驱动基因,提供了超越传统差异表达分析对复杂疾病的新见解.
科学领域:
- 基因组学就是基因组学.
- 系统生物学 系统生物学
- 生物信息学是一种生物信息学.
背景情况:
- 网络推断模型生物相互作用 (转录,信号,代谢) 了解疾病的发病因子.
- 基于机器学习 (ML) 的推断模型在发现基因组数据中的复杂模式方面表现有前途.
- 现有的统计模型往往难以识别复杂疾病的致病因素.
研究的目的:
- 介绍CoVar,一种ML框架,用于识别驱动扰乱基因表达的中心基因.
- 通过关注网络相互作用变化,将CoVar的方法与传统的差异表达基因 (DEGs) 分析区分开来.
- 揭示生物状态中的基因表达变化背后的调节动态和协调过程.
主要方法:
- CoVar使用ML来识别具有改变表达网络相互作用配置文件的变异基因.
- 它进一步确定了变异基因的最近邻居中的核心基因.
- 该框架使用模拟数据和酵母表达数据与线粒体基因组删除进行了验证.
主要成果:
- CoVar有效地捕捉了基因表达数据中的内在变异性和模块化.
- 它成功地确定了现有的差异分析方法遗漏的关键驱动基因.
- 这项研究表明,CoVar能够提供对监管动态的洞察力.
结论:
- CoVar为了解基因调节网络和疾病机制提供了一种新的方法.
- 识别变异基因和核心基因可以更深入地了解协调的监管过程.
- 这种基于机器学习的框架促进了对复杂疾病研究的基因组数据的分析.
更多相关视频
10:44Inherent Dynamics Visualizer, an Interactive Application for Evaluating and Visualizing Outputs from a Gene Regulatory Network Inference Pipeline
Published on: December 7, 2021
2.1K
07:23Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome
Published on: June 15, 2016
8.5K
相关概念视频
01:23Regulation of Expression at Multiple Steps
902
The gene expression in cells is regulated at different stages: (i) transcription, (ii) RNA processing, (iii) RNA localization, and (iv) translation. Transcriptional regulation is mediated by regulatory proteins such as transcription factors, activators, or repressors—these control gene expression by initiating or inhibiting the transcription of genes. Once a precursor or pre-mRNA is produced, it undergoes post-transcriptional modification, including 5' capping, splicing, and the...
902
02:24Regulation of Expression Occurs at Multiple Steps
3.0K
3.0K
02:33Combinatorial 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...
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...
8.3K
02:23Master 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
02:13Cooperative Binding of Transcription Regulators
6.4K
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...
6.4K
02:02Cis-regulatory Sequences
9.9K
Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
9.9K