GeOKG:用于基因本体学和基因的几何意识知识图嵌入
Chang-Uk Jeong1,2,3, Jaesik Kim3,4, Dokyoon Kim2,3
1Department of Software and Computer Engineering, Ajou University, Suwon, 16499, South Korea.
Bioinformatics (Oxford, England)
|April 11, 2025
概括
几何意识知识图嵌入 (GeOKG) 使用几何交互来建模基因本体学 (GO) 层次结构. 这种方法通过更好地捕捉复杂的生物关系来改善蛋白质-蛋白质相互作用的预测.
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
- 网络科学 网络科学
背景情况:
- 对于基因本体学 (GO) 和基因本体学注释 (GOA) 的深度学习,表示学习有助于预测蛋白质-蛋白质相互作用等生物任务.
- 现有的方法将GO和GOA嵌入单个几何空间中,这对于GO的复杂,非单调的层次结构是不够的.
研究的目的:
- 为了解决模拟GO的等级结构中的局限性.
- 开发一种新的方法来增强GO和GOA的代表性学习.
主要方法:
- 拟议的几何意识知识图嵌入 (GeOKG) 方法.
- 在训练期间利用各种几何表示之间的几何相互作用.
- 更有效地模拟了GO的复杂层次结构.
主要成果:
- GeOKG有效地模拟了GO的复杂等级结构.
- 在政府级别的实验证明了几何相互作用的好处.
- 在基因层面上,GeOKG在蛋白质-蛋白质相互作用预测方面表现优于现有的方法.
结论:
- 几何交互是嵌入异质生物医学网络的一个有希望的方法.
- GeOKG增强了GO和GOA对下游生物任务的表示学习.
- 这些发现突出了改善生物网络分析的新方向.
相关概念视频
02:07Organization of Genes
68.2K
Overview
68.2K
01:57Gene Families
2.5K
2.5K
01:30Structure of a Gene
12.3K
A gene is the fundamental unit of heredity. Every individual has two copies of each gene, one inherited from each parent. Although most people contain the same genes, there is a small fraction that is slightly different amongst people. A gene with a small difference in its sequence of DNA bases forms different alleles, contributing to different phenotypes.
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
However, only 1% of the DNA is composed of genes that encode proteins; the rest, 99% is non-coding DNA. This non-coding DNA performs...
12.3K
03:36Genome Annotation and Assembly
18.7K
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.
18.7K
02:05Gene Evolution - Fast or Slow?
7.0K
The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
In contrast, regions which code...
7.0K
02:02Genomics
35.3K
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...
35.3K