混合表示学习为人类m6A修改与染色体水平的概括性修改
Muhammad Tahir1, Sheela Ramanna1, Qian Liu1,2
1Department of Applied Computer Science, The University of Winnipeg, Winnipeg, MB R3B 2E9, Canada.
Bioinformatics advances
|July 25, 2025
概括
我们开发了新的深度学习模型来预测mRNA中的N6-甲基氨酸 (m6A) 位点. 我们的模型表现出更好的性能和概括性,优于现有方法,特别是在染色体独立评估中.
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
- 基因组学就是基因组学.
背景情况:
- N6-甲基氨酸 (m6A) 是一种关键的mRNA修饰,可以在转录后调节基因表达.
- 现有的m6A位点预测的深度学习模型由于数据集分割方法,往往缺乏染色体水平的概括性.
研究的目的:
- 开发和评估新的混合深度学习模型,以准确和可概括的m6A站点预测.
- 用随机和染色体外交叉验证策略来评估模型性能.
主要方法:
- 提出了两种混合深度学习模型,集成k-mer序列特征和使用CNN的上下文嵌入.
- 用随机分割和留下一个染色体的策略进行评估模型,以进行可靠的评估.
- 与最先进的m6A-TCPred模型进行性能比较.
主要成果:
- 两种拟议的模型在关键指标上都表现优于m6A-TCPred.
- 混合深度模型在随机分割验证中实现了最高的准确性.
- 混合模型在Leave-One-Chromosome-Out验证中表现出优越的概括性,这表明在染色体独立的环境中,深层全球表示的潜在过拟合.
结论:
- 开发的混合模型提供了改进的m6A站点预测准确性和概括性.
- 离开一个染色体的验证对于评估m6A预测器的真正稳定性至关重要.
- 结果为设计更可靠的m6A预测工具提供了洞察力.
相关概念视频
Mismatch Repair
5.2K
Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
The Mutator Protein Family Plays a Key Role in DNA Mismatch Repair
The human genome has more than 3 billion base pairs of DNA per cell. Prior to cell division, that vast amount of genetic...
5.2K
Inheritance of Chromatin Structures
6.6K
Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying...
6.6K
Heterochromatin
14.6K
The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at...
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at...
14.6K
Gene Conversion
10.0K
Other than maintaining genome stability via DNA repair, homologous recombination plays an important role in diversifying the genome. In fact, the recombination of sequences forms the molecular basis of genomic evolution. Random and non-random permutations of genomic sequences create a library of new amalgamated sequences. These newly formed genomes can determine the fitness and survival of cells. In bacteria, homologous and non-homologous types of recombination lead to the evolution of new...
10.0K
Hybrid Zones
20.2K
Hybrid zones are narrow regions where two closely related species interact, mate, and produce hybrids. Relative to either parent species, hybrids may possess distinct phenotypic or genetic differences that impact their survival and reproductive success. The genetic variances introduced by hybridization influence species diversity and speciation processes within the hybrid zone.
20.2K
Synteny and Evolution
3.4K
John H. Renwick first coined the term “synteny” in 1971, which refers to the genes present on the same chromosomes, even if they are not genetically linked. The species with common ancestry tend to show conserved syntenic regions. Therefore, the concept of synteny is nowadays used to describe the evolutionary relationship between species.
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
Around 80 million years ago, the human and mice lineages diverged from the common ancestor. During the course of evolution, the ancestral...
3.4K


