多重接触:对基因组,转录组和蛋白质组的整合性分析确定了复杂特征的因果机制
Jeffrey Okamoto1, Xianyong Yin2,3, Brady Ryan2
1Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI, 48109, USA. jokamoto@umich.edu.
Genome biology
|February 3, 2025
概括
我们开发了Multi-INTACT,这是一种使用遗传数据识别因果基因及其产物 (RNA和蛋白质) 的新算法. 这种方法提高了准确性,并比以前的方法识别了更多的代谢物因果基因.
科学领域:
- 遗传学 遗传学是一种遗传学.
- 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:
- 识别复杂特征的因果基因是一个挑战.
- 整合多种分子数据类型,如RNA和蛋白质水平,可以改善因果推理.
研究的目的:
- 引入Multi-INTACT,这是一个用于多omics集成的新算法.
- 加强因果基因及其特定基因产物的识别.
主要方法:
- 开发了多INTACT算法来建模多个基因产品 (RNA和蛋白质).
- 进行模拟以评估Multi-INTACT的性能与现有方法相比.
- 应用Multi-INTACT对1408种代谢物的全基因组关联研究 (GWAS) 数据,整合GTEx表达和英国生物银行蛋白质定量特征位点 (QTL) 数据.
主要成果:
- 多INTACT在模拟中显示出更高的统计能力,并保持了校准的错误发现率.
- 该算法成功识别了真正的因果基因产物.
- 与单分子分析相比,对代谢物GWAS的应用揭示了52-109%更多的因果基因.
- 发现RNA和蛋白质水平都与大多数已识别的因果基因有关.
结论:
- 多INTACT提供了一种强大的方法,用于在遗传学研究中整合多omics.
- 该算法显著改善了因果基因及其产品的发现,用于复杂的特征,如代谢物水平.
- 整合转录基因和蛋白质基因数据对于全面的因果基因鉴定至关重要.
更多相关视频
08:51Author Spotlight: Integrated Multi-Omics Analysis for Unveiling Multicellular Immune Signatures in Clinical Heart Attack Cohorts
Published on: September 20, 2024
1.1K
04:41Mapping Alzheimer's Disease Variants to Their Target Genes Using Computational Analysis of Chromatin Configuration
Published on: January 9, 2020
18.9K
相关概念视频
Proteomics
7.2K
A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
7.2K
Genomics
35.8K
Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
35.8K
Epistasis Analysis
4.9K
Although Mendel chose seven unrelated traits in peas to study gene segregation, most traits involve multiple gene interactions that create a spectrum of phenotypes. When the interaction of various genes or alleles at different locations influences a phenotype, this is called epistasis. Epistasis often involves one gene masking or interfering with the expression of another (antagonistic epistasis). Epistasis often occurs when different genes are part of the same biochemical pathway. The...
4.9K
Genome Annotation and Assembly
18.8K
The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
18.8K
Genome-wide Association Studies-GWAS
12.4K
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...
GWAS does not require the identification of the target gene involved in...
12.4K
Ribosome Profiling
3.5K
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.
The technique...
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.
The technique...
3.5K
