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相关概念视频

Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
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Regulation of Expression at Multiple Steps01:23

Regulation of Expression at Multiple Steps

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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...
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Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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General Transcription Factors01:30

General 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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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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相关实验视频

Updated: Jun 7, 2025

A Pathway Association Study Tool for GWAS Analyses of Metabolic Pathway Information
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TIPS:一种全新的通路引导的联合模型,用于转录组范围内的关联研究.

Neng Wang1,2, Zhenyao Ye3, Tianzhou Ma2

  • 1Department of Mathematics, University of Maryland, College Park, MD 20742, United States.

Briefings in bioinformatics
|November 16, 2024
PubMed
概括

这项研究介绍了TIPS,这是一种通过整合基因路径来分析复杂特征的新方法. TIPS识别了与血压和大脑衰老等特征相关的关键基因和途径,提供了比传统方法更深入的生物学见解.

关键词:
在EM算法中,EM算法生物通道是生物通道.稀疏的群体拉索拉索是一个稀疏的群体.转录组范围的关联研究研究.

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科学领域:

  • 基因组学和生物信息学
  • 统计遗传学 统计遗传学
  • 复杂特征分析 复杂特征分析

背景情况:

  • 全基因组关联研究 (GWAS) 识别了与疾病相关的单核酸多态 (SNP),但许多位于非编码区域,阻碍了解释.
  • 全转录组关联研究 (TWAS) 通过将SNP与基因表达联系起来来提高解释性,但通常会产生缺乏明确生物主题的基因列表.
  • 单变TWAS努力揭示复杂的多基因特征的潜在生物机制.

研究的目的:

  • 开发一种新的多变体TWAS方法,即TIPS (包含途径或基因组信息的全转录组推断),用于识别与复杂多基因特征相关的基因和途径.
  • 通过将路径信息直接纳入关联模型,提高TWAS发现的生物解释性.
  • 加强对生物相关途径和基因的识别,这些基因可能会被传统的单变型TWAS遗漏.

主要方法:

  • 开发了一种多变量TWAS方法 (TIPS),该方法共同模拟归算和关联步骤.
  • 整合了稀疏组激光惩罚,以实现在基因和途径层面同时进行选择.
  • 在处罚概率模型中,利用预期最大化算法进行参数估计.

主要成果:

  • 应用 TIPS 复杂的特征,包括缩血压,腹缩血压和白质大脑年龄差距在英国生物银行数据.
  • 确定了与这些特征相关的关键,生物相关的途径和基因,这些特征是传统的单变TWAS与途径丰富分析相结合无法检测的.
  • 模拟表明,在各种遗传性和遗传架构场景中,TIPS在特征选择,统计能力和预测准确性方面优于已建立的TWAS方法.

结论:

  • TIPS提供了一种强大的方法,通过整合基因表达和通路信息来剖析复杂的多基因特征的遗传结构.
  • 该方法增强了生物学上有意义的途径和基因的发现,为特征相关机制提供了更深入的见解.
  • 与单变TWAS相比,TIPS代表了显著的进步,为复杂的特征遗传学提供了更好的性能和可解释性.