相关实验视频

Updated: May 5, 2026

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

基于机器学习的PlantCdMiner预测和实验验证植物中对敏感基因的验证

Chaoqun Xu¹, Ling Sun¹, Lu-Dan Zhang²

¹Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen 361104, China.

Journal of hazardous materials

|May 16, 2025

概括

这项研究使用机器学习预测植物中的反应基因,使跨物种分析和识别MYB转录因子 (TFs) 成为应激适应的关键. 一个新的工具,PlantCdMiner,有助于这个预测和 cis-regulatory 元素可视化.

科学领域:

植物生物学植物生物学
基因组学就是基因组学.
生物信息学是一种生物信息学.

背景情况:

植物使用适应机制来应对等环境压力因素.
基因表达调节对于植物非生物应激反应至关重要.
同源基因可以表现出不同的应激反应,限制了传统的预测方法.

研究的目的:

开发一种机器学习方法,用于预测对敏感基因.
评估跨物种转录组数据对压力基因预测的有用性.
为了确定关键的调节元素和转录因子涉及压力.

主要方法:

随机森林算法用于监督对敏感基因的分类.
对多种植物物种 (Arabidopsis thaliana,Avicennia marina,Hordeum vulgare,Nicotiana tabacum) 的基因序列特征的分析.
交叉调节元素分析和实验验证 (酵母单杂交,双露西法酶记者测试).

主要成果:

机器学习模型准确地预测了物种内部和跨物种的敏感基因.
来自经过充分研究的物种的转录组数据可以预测其他物种的应激反应基因.
MYB转录因子 (TF) 被确定为应激反应的关键调节者.
实验验证证了MYB TF Am06526在调节AmPCR2表达中的作用.

结论:

机器学习有效地预测了植物对敏感基因,克服了基于同质学的方法的局限性.
跨物种预测是可行的,利用模型生物的数据.
MYB TFs是植物应激适应的关键参与者.
植物CdMiner工具为压力基因预测和分析提供了宝贵的资源.

关键词:

机器学习机器学习在R/Shiny中使用.在RNA-seqqq.调节应激的规范性这些是cis-regulatory元素.

更多相关视频

Real-time In Vivo Recording of Arabidopsis Calcium Signals During Insect Feeding Using a Fluorescent Biosensor

Real-time In Vivo Recording of Arabidopsis Calcium Signals During Insect Feeding Using a Fluorescent Biosensor

Published on: August 15, 2017

CcCIPK14 Gene Function Analysis to Illuminate the Efficient Root Transgenic System

CcCIPK14 Gene Function Analysis to Illuminate the Efficient Root Transgenic System

Published on: September 23, 2021

相关概念视频

C4 Pathway and CAM

C4 Pathway and CAM

Most plants use the C3 pathway for carbon fixation. However, some plants, such as sugar cane, corn, and cacti that grow in hot conditions, use alternative pathways to fix carbon and conserve energy loss due to photorespiration. Photorespiration is the process that occurs when the oxygen concentration is high. Under such conditions, the rubisco enzyme in the Calvin cycle binds O2 instead of CO2, which halts photosynthesis and consumes energy.
C4 Pathway
The C4 pathway is used by plants such as...

Key Elements for Plant Nutrition

Key Elements for Plant Nutrition

Like all living organisms, plants require organic and inorganic nutrients to survive, reproduce, grow and maintain homeostasis. To identify nutrients that are essential for plant functioning, researchers have leveraged a technique called hydroponics. In hydroponic culture systems, plants are grown—without soil—in water-based solutions containing nutrients. At least 17 nutrients have been identified as essential elements required by plants. Plants acquire these elements from the...

Cell Signaling in Plants

Cell Signaling in Plants

Plant cells communicate to coordinate their cycle of growth, flowering and fruiting, and activities in roots, shoots, and leaves in response to the changing environmental conditions. Plant signaling is distinct from animal signaling. Plants primarily utilize enzyme-linked receptors, whereas the largest class of cell-surface receptors in animals are G-protein coupled receptors (GPCRs). Unlike animals, receptor tyrosine kinases are rare in plants. Instead, plants have a diverse class of...