一个基于深度学习的框架,通过整合多omics和临床数据来预测结肠癌中与生存相关的群体
Siamak Salimy1, Hossein Lanjanian2, Karim Abbasi3
1Laboratory of System Biology and Bioinformatics (LBB), Department of Bioinformatics, University of Tehran, Kish International Campus, Kish, Iran.
Heliyon
|July 17, 2023
概括
这项研究引入了一种机器学习方法,用于整合多omics数据,用于结肠癌患者的预后. 超参数优化的自编码方法有效地识别了生存子组和相关基因.
科学领域:
- 在瘤学瘤学.
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
背景情况:
- 准确的预后分类对于定制癌症治疗策略至关重要.
- 多omics数据集成为识别患者生存子组提供了强大的工具.
- 结肠癌患者数据需要先进的分析方法来获得预后见解.
研究的目的:
- 引入和评估一种机器学习方法,用于整合结肠癌中的多omics数据 (RNA-seq,DNA甲基化,临床数据).
- 为了比较超参数优化自编码器 (HPOAE) 与其他方法在确定患者生存依赖性的性能.
- 确定关键基因和与结肠癌患者生存相关的微RNA.
主要方法:
- 利用TCGA RNA-seq基因表达,DNA甲基化和来自368名结肠癌患者的临床数据,以及232个样本的外部验证集.
- 应用了三种数据集成方法:超参数优化自编码器 (HPOAE),正常自编码器和处罚主要组件分析 (PPCA).
- 采用COX危险模型,同时进行数据集成和生存估计.
主要成果:
- 与其他方法相比,HPOAE方法在识别生存子组和相关基因方面表现优越.
- HPOAE的Log Rank Mantel-Cox值为14.27±2,而Breslow-Generalized Wilcoxon值为13.13±1. HPOAE的Log Rank Mantel-Cox值为14.27±2,而Breslow-Generalized Wilcoxon值为13.13±1. HPOAE的Log Rank Mantel-Cox值为14.27±2,而Breslow-Generalized Wilcoxon值为13.13±1. HPOAE的Log Rank Mantel-Cox值为14.27±2,而Breslow-Generalized Wilcoxon值为13.13±1. HPOAE的Log Rank Mantel-Cox值为14.27±2.
- 确定了10个miRNA,11个甲基化基因和28个mRNA,包括针对ZMYM1和tp53.5的hsa-miR-485-5p.
结论:
- 通过整合多omics数据,HPOAE方法显示了通过整合多omics数据来改善结肠癌的预后分类的巨大潜力.
- 已识别的基因和miRNA,如hsa-miR-485-5p,为结肠癌预后提供了潜在的生物标志物.
- 临床和实验验证是必要的,以确认计算发现及其临床实用性.
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