一个基于生存的基因组丰富分析的R包
Xiaoxu Deng1, Jeffrey A Thompson1
1University of Kansas Medical Center.
Research square
|October 16, 2023
概括
基于生存的基因组丰富分析 (SGSEA) 通过使用危险比率来帮助识别与疾病生存相关的生物功能. 这种在R包和Shiny应用程序中提供的方法有助于发现脏清细胞癌的疾病变异途径.
科学领域:
- 生物信息学是一种生物信息学.
- 基因组学就是基因组学.
- 翻译医学是一种翻译医学.
背景情况:
- 功能丰富分析通常评估实验差异.
- 了解转录组变异与生存结果的联系在疾病研究中至关重要.
- 标准基因组丰富分析 (GSEA) 使用日志折叠变化,不适合存活数据.
研究的目的:
- 引入基于生存的基因组丰富分析 (SGSEA) 来将生物功能与疾病生存联系起来.
- 开发一个R包和一个名为SGSEA的闪亮应用程序,用于这种新的分析.
- 使用脏清细胞癌 (KIRC) 数据集来证明SGSEA的实用性.
主要方法:
- 通过将日志折变更替换为基因排名的危险比,进行调整基因组丰富分析 (GSEA).
- 开发了一个R包和Shiny App (SGSEA) 用于执行基于生存的基因组丰富分析.
- 将SGSEA应用于KIRC数据集,以确定与生存相关的途径.
主要成果:
- 鉴定了与基因丰富的途径,显示与死亡率相关的转录增加 (NES > 0,调整后的p值<0.15).
- 证实了这些丰富的途径以前与KIRC存活相关.
- 证明了SGSEA在识别疾病生存的生物相关途径方面的价值.
结论:
- SGSEA提供了一种有价值的方法,用于识别与患者存活相关的疾病变异途径.
- 对于研究人员来说,SGSEA R包和Shiny App提供了一个方便的工具.
- 这种方法补充了标准GSEA,通过结合生存数据来增强生物洞察力.
相关概念视频
Comparing the Survival Analysis of Two or More Groups
202
Survival analysis is a cornerstone of medical research, used to evaluate the time until an event of interest occurs, such as death, disease recurrence, or recovery. Unlike standard statistical methods, survival analysis is particularly adept at handling censored data—instances where the event has not occurred for some participants by the end of the study or remains unobserved. To address these unique challenges, specialized techniques like the Kaplan-Meier estimator, log-rank test, and...
202
Introduction To Survival Analysis
252
Survival analysis is a statistical method used to study time-to-event data, where the "event" might represent outcomes like death, disease relapse, system failure, or recovery. A unique feature of survival data is censoring, which occurs when the event of interest has not been observed for some individuals during the study period. This requires specialized techniques to handle incomplete data effectively.
The primary goal of survival analysis is to estimate survival time—the time...
The primary goal of survival analysis is to estimate survival time—the time...
252
Cancer Survival Analysis
359
Cancer survival analysis focuses on quantifying and interpreting the time from a key starting point, such as diagnosis or the initiation of treatment, to a specific endpoint, such as remission or death. This analysis provides critical insights into treatment effectiveness and factors that influence patient outcomes, helping to shape clinical decisions and guide prognostic evaluations. A cornerstone of oncology research, survival analysis tackles the challenges of skewed, non-normally...
359
Assumptions of Survival Analysis
149
Survival models analyze the time until one or more events occur, such as death in biological organisms or failure in mechanical systems. These models are widely used across fields like medicine, biology, engineering, and public health to study time-to-event phenomena. To ensure accurate results, survival analysis relies on key assumptions and careful study design.
149
Parametric Survival Analysis: Weibull and Exponential Methods
451
Parametric survival analysis models survival data by assuming a specific probability distribution for the time until an event occurs. The Weibull and exponential distributions are two of the most commonly used methods in this context, due to their versatility and relatively straightforward application.
Weibull Distribution
The Weibull distribution is a flexible model used in parametric survival analysis. It can handle both increasing and decreasing hazard rates, depending on its shape parameter...
Weibull Distribution
The Weibull distribution is a flexible model used in parametric survival analysis. It can handle both increasing and decreasing hazard rates, depending on its shape parameter...
451
Survival Tree
89
Survival trees are a non-parametric method used in survival analysis to model the relationship between a set of covariates and the time until an event of interest occurs, often referred to as the "time-to-event" or "survival time." This method is particularly useful when dealing with censored data, where the event has not occurred for some individuals by the end of the study period, or when the exact time of the event is unknown.
Building a Survival Tree
Constructing a...
Building a Survival Tree
Constructing a...
89


