使用知识图来推断植物中的基因表达
Anne E Thessen1, Laurel Cooper2, Tyson L Swetnam3
1Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, United States.
Frontiers in artificial intelligence
|June 29, 2023
概括
了解物种间的基因表达是适应气候变化的关键. 这项研究表明,虽然同源基因具有共同的祖先,但预测表型需要在知识图中整合cis和跨调节元素.
科学领域:
- 植物生物学 植物生物学
- 生物信息学是一种生物信息学.
- 基因组学就是基因组学.
背景情况:
- 气候变化影响生态系统和农业,需要适应战略.
- 了解跨物种的基因型-环境-表型 (G×E×P) 动态对于弹性至关重要.
- 基因调节网络对于预测表型至关重要,物种之间的知识转移可以加速这种理解.
研究的目的:
- 开发一个知识图 (KG),整合基因表达,分子相互作用和功能.
- 通过同类推断来研究基因型-环境-表型动态,用于跨物种知识应用.
- 评估cis和跨调节元素在干旱压力下预测同源基因表达模式中的作用.
主要方法:
- 使用Planteome和EMBL-EBI表达式图谱的数据构建了一个KG.
- 在干旱条件下分析了Arabidopsis thaliana*和Populus trichocarpa*的基因表达数据.
- 利用图表查询来识别同源基因,并分析它们的cis-regulatory区域.
主要成果:
- 确定了16个同类基因对,分别是*A. thaliana*和*P. trichocarpa*,在干旱期间表达模式不同.
- 具有类似表达干旱反应的同类基因表现出保存的cis调节区域和跨元素相互作用.
- 具有相反表达模式的同源基因在调节元素中显示出分歧.
结论:
- 预测基因表达和表型的同质推断需要仔细整合cis和跨调节信息.
- 知识图可以促进基因调节网络的跨物种比较.
- 这种方法有助于理解和预测植物对干旱等环境变化的反应.
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