FUN-PROSE:一种深度学习方法,用于预测真菌中特定条件的基因表达
Ananthan Nambiar1,2, Veronika Dubinkina1,2,3, Simon Liu2,4
1Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois, United States of America.
PLoS computational biology
|November 16, 2023
概括
我们开发了FUN-PROSE,这是一个深度学习模型,使用促进器序列和转录因子水平预测真菌中的基因表达变化. 这通过揭示特定条件的基因调节来推进代谢工程.
科学领域:
- 基因组学就是基因组学.
- 系统生物学 系统生物学
- 计算生物学 计算生物学
背景情况:
- 了解细胞状态需要在各种条件下分析全基因组mRNA水平.
- 化学生产的真菌的代谢工程需要准确预测特定条件的基因表达.
- 以前的深度学习模型经常预测平均基因表达,忽略了特定条件的变异.
研究的目的:
- 开发一个深度学习模型,FUN-PROSE,用于预测真菌中的差异基因表达.
- 利用促进子序列和转录因子水平作为预测条件特定基因表达的输入.
- 解释用于发现新型调节元件和转录因子-基因相互作用的模型.
主要方法:
- 开发了FUN-PROSE,一个深度学习模型.
- 在三种真菌物种上训练并测试了模型.
- 使用序列图案提取和特征重要性分析解释模型.
主要成果:
- 在预测和观察到的条件特定基因表达之间实现了高相关性 (高达0.85).
- 识别了与可变基因表达相关的促进子序列动机.
- 将特定的转录因子与它们的基因标联系起来,揭示了已知的和新的相互作用.
结论:
- FUN-PROSE准确地预测了真菌中特定条件的基因表达.
- 模型解释揭示了生物学相关的序列动机和转录因子-基因相互作用.
- 这些发现支持了真菌代谢工程和监管网络发现的进展.
相关概念视频
What is Gene Expression?
Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
What is Gene Expression?
Overview
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
Gene expression is the process in which DNA directs the synthesis of functional products, that is, proteins. Cells can regulate gene expression at various stages. It allows organisms to generate different cell types and enables cells to adapt to internal and external factors.
Genetic Information Flows from DNA to RNA to Protein
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is made up of nucleotides and proteins consist of amino...
Cell Specific Gene Expression
Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
What is Gene Expression?
A gene is a stretch of DNA that serves as the blueprint for functional RNAs and proteins. Since DNA is comprised of nucleotides and proteins are comprised of amino acids, a mediator is required to convert the information encoded in DNA into proteins. This mediator is the messenger RNA (mRNA). mRNA copies the blueprint from DNA by a process called transcription. In eukaryotes, transcription occurs in the nucleus by complementary base-pairing with the DNA template. The mRNA is then processed and...
Cell Specific Gene Expression
Multicellular organisms contain a variety of structurally and functionally distinct cell types, but the DNA in all the cells originated from the same parent cells. The differences in the cells can be attributed to the differential gene expression. Liver cells, whose functions include detoxification of blood, production of bile to metabolize fats, and synthesis of proteins essential for metabolism, must express a specific set of genes to perform their functions. Gene expression also varies with...
Gene Regulation During Sporulation
Sporulation is a complex developmental process that allows certain Gram-positive bacteria, such as Bacillus subtilis and Clostridium species, to survive extreme environmental conditions. This process is tightly regulated by a series of signaling cascades and transcriptional controls, ensuring the formation of a highly resistant endospore.Sporulation is triggered by unfavorable conditions, such as nutrient depletion, and is governed by a phosphorelay system. One of the sensor kinases, such as...


