在疾病建模中对基因与环境相互作用进行分层多标签分类.
Jingmao Li1, Qingzhao Zhang1,2, Shuangge Ma3
1Department of Statistics and Data Science, School of Economics, Xiamen University, Fujian, China.
Statistics in medicine
|January 27, 2025
概括
本研究引入了一种用于分析复杂疾病中的基因环境 (G-E) 相互作用的新方法,特别是用于分级多标签分类. 该方法有效处理未标记的数据,改善疾病结果预测和特征选择.
科学领域:
- 生物医学信息学 生物医学信息学
- 遗传学 遗传学 是一个
- 计算生物学 计算生物学
背景情况:
- 基因-环境 (G-E) 相互作用对于理解疾病病因而言至关重要,而不仅仅是个体遗传或环境因素.
- 现有的GE相互作用分析往往忽略了层次的多标签分类和半监督学习场景.
- 在现实世界生物医学研究中常见的未标记的数据经常被当前的层次多标签分类方法排除在外.
研究的目的:
- 开发一种新的计算框架,用于在层次的多标签分类环境中分析GE相互作用.
- 用半监督方法解决将未标记的数据纳入GE相互作用分析的挑战.
- 为识别由GE相互作用影响的复杂疾病结果提供一个强大的方法.
主要方法:
- 开发了一种新的方法,用于两层层次的等级反应,包括GE相互作用.
- 采用了两步惩罚性估计策略.
- 一个高效的预期最大化 (EM) 算法被用于参数估计.
主要成果:
- 与现有方法相比,拟议的方法在分类准确性和特征选择方面都表现出优异的性能.
- 模拟证实了开发算法的有效性和稳定性.
- 适用于癌症基因组图谱 (TCGA) 肺癌数据的应用验证了其实际实用性.
结论:
- 这项研究通过引入对层次多标签分类的多功能框架,弥补了GE相互作用分析中的重大知识差距.
- 开发的方法为剖析由GE相互作用影响的复杂疾病机制提供了一个强大的工具.
- 该方法有效地处理半监督学习场景,增强对现实世界生物医学数据的适用性.
相关概念视频
Gene-Environment Interactions
247
Gene expression is a dynamic process that is significantly influenced by environmental factors. This interaction underlies the complex nature of biological development and the phenotypic differences observed among individuals, even among those with identical genetic makeups. Factors such as radiation, temperature, behavior, nutrition, and stress play pivotal roles in determining how genes are expressed. The concept of the reaction range is central to understanding this interaction. It posits...
247
Background and Environment Affect Phenotype
6.4K
Although the genetic makeup of an organism plays a major role in determining the phenotype, there are also several environmental factors, such as temperature, oxygen availability, presence of mutagens, that can alter an organism’s phenotype.
An example of how genetic background affects phenotype can be seen in horses. The Extension gene in horses is responsible for their coat color. A wild-type gene (EE) produces black pigment in the coat, while a mutant gene (ee) produces red pigment. A...
An example of how genetic background affects phenotype can be seen in horses. The Extension gene in horses is responsible for their coat color. A wild-type gene (EE) produces black pigment in the coat, while a mutant gene (ee) produces red pigment. A...
6.4K
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
Pleiotropy
39.6K
Pleiotropy is the phenomenon in which a single gene impacts multiple, seemingly unrelated phenotypic traits. For example, defects in the SOX10 gene cause Waardenburg Syndrome Type 4, or WS4, which can cause defects in pigmentation, hearing impairments, and an absence of intestinal contractions necessary for elimination. This diversity of phenotypes results from the expression pattern of SOX10 in early embryonic and fetal development. SOX10 is found in neural crest cells that form melanocytes,...
39.6K
Genetic Lingo
100.3K
Overview
100.3K
Epistasis
45.6K
In addition to multiple alleles at the same locus influencing traits, numerous genes or alleles at different locations may interact and influence phenotypes in a phenomenon called epistasis. For example, rabbit fur can be black or brown depending on whether the animal is homozygous dominant or heterozygous at a TYRP1 locus. However, if the rabbit is also homozygous recessive at a locus on the tyrosinase gene (TYR), it will have an unshaded coat that appears white, regardless of its TYRP1...
45.6K


