在转录因子多重体上嵌入结构前置使基因调节网络和潜在活动推断的透明模型架构成为可能
Andreas Tjärnberg1,2,3,4,5, Maggie Beheler-Amass6,7, Christopher A Jackson6,7
1Center for Developmental Genetics, New York University, New York, NY, 10003, USA. andreas.tjarnberg@fripost.org.
Genome biology
|January 18, 2024
概括
我们开发了SupirFactor,这是一种新的深度学习框架,用于推断基因调节网络 (GRNs) 和转录因子活性 (TFA). 这种方法通过提供复杂的监管相互作用的可解释模型来改善生物洞察力.
科学领域:
- 计算生物学 计算生物学
- 系统生物学 系统生物学
- 基因组学就是基因组学.
背景情况:
- 基因调节网络 (GRN) 建模受到全基因组转录因子活性 (TFA) 测量不足的阻碍,使共变性和调节相互作用之间的区别变得复杂.
- 明确估计TFA将GRN推断和TFA估计断开,未能捕捉诸如上下文转录因子相互作用等更高阶特征.
- 深度学习模型可以捕捉复杂的相互作用,但往往缺乏隐藏特征的解释性和明确的生物含义.
研究的目的:
- 引入SupirFactor,这是一个基于自编码器的新型框架,用于基于结构的GRN推断和TFA估计.
- 开发一种解释度量,解释相对变异 (ERV),用于评估推断的GRNs的质量和生物相关性.
- 评估SupirFactor在各种数据集和生物环境中的性能和生物解释性.
主要方法:
- 开发了SupirFactor,这是一个自动编码框架,集成GRN结构和隐藏因子活动进行推断.
- 使用解释相对方差 (ERV) 作为解释GRN模型和潜在特征的度量.
- 应用SupirFactor以建模GRNs并估计Saccharomyces cerevisiae和人体外围血液单核细胞 (PBMC) 数据集中的TFA.
主要成果:
- 与最先进的GRN推断方法相比,SupirFactor表现良好.
- 评估了作为TFA的代理的潜在特征活性,揭示了S. cerevisiae和PBMC中的生物功能.
- 该框架成功地集成了GRN推断和TFA估计,考虑了复杂的监管相互作用.
结论:
- SupirFactor框架为GRN建模和TFA估计提供了一个可解释的方法.
- SupirFactor使用潜在因子活性促进生物分析和途径解释.
- 该模型成功地从大型单细胞数据集中获得了新的功能和监管见解.
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