一个基于生存的基因组丰富分析的R包
Xiaoxu Deng1, Jeffrey Thompson1,2
1Department of Biostatistics & Data Science, University of Kansas Medical Center, Kansas City, KS, United States of America.
PeerJ
|July 15, 2025
概括
基于生存的基因组丰富分析 (SGSEA) 确定与疾病生存相关的生物功能. 这个新的R包和Shiny应用程序利用危险比率来找到与死亡率相关的途径,帮助癌症研究.
科学领域:
- 生物信息学是一种生物信息学.
- 计算生物学 计算生物学
- 基因组学就是基因组学.
背景情况:
- 功能性丰富分析通常评估实验差异,而不是与生存等健康结果的直接联系.
- 了解转录组变异与生存的关系对于疾病研究至关重要.
研究的目的:
- 引入基于生存的基因组丰富分析 (SGSEA) 以确定与疾病生存相关的生物功能.
- 开发和介绍一个R包和Shiny应用程序,用于执行SGSEA.
主要方法:
- 通过使用危险比率而不是日志折叠变化来排名基因,SGSEA适应了基因组丰富分析 (GSEA).
- 该方法使用脏清细胞癌 (KIRC) 的研究来证明.
主要成果:
- 通过基因丰富的途径显示与死亡相关的转录增加 (NES>0,调整后的p值<0.15).
- 这些丰富的途径以前与KIRC存活率相关,验证了SGSEA方法.
结论:
- SGSEA提供了一种有价值的方法,可以快速识别影响生存的疾病变异途径.
- 开发的R包和Shiny应用程序为研究人员提供了可访问的工具,以补充标准GSEA.
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