单细胞时间序列的变化推理.
Bingxian Xu1,2, Rosemary Braun1,2,3,4,5,6
1Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA.
bioRxiv : the preprint server for biology
|September 11, 2024
概括
深度学习算法SNOW将单细胞RNA测序时间序列数据分解,以分离时间依赖和独立因素. 这使得能够准确地注释细胞类型,并对基因表达动态进行可靠的分析,而不会丢失信息.
科学领域:
- 计算生物学 计算生物学
- 基因组学就是基因组学.
- 生物信息学是一种生物信息学.
背景情况:
- 单细胞RNA测序 (scRNA-seq) 在单细胞分辨率下提供了对全基因组表达动态的洞察.
- 当基因表达受到时间和细胞身份的影响时,分析scRNA-seq数据变得复杂,复杂化了细胞类型注释和动态建模.
研究的目的:
- 介绍SNOW (Single cell flOW map),一个深度学习算法,旨在解构单细胞时间序列数据.
- 为了实现准确的细胞类型注释和模型细胞类型依赖的基因表达动态.
主要方法:
- 在scRNA-seq数据中,SNOW使用深度学习框架来分离时间依赖和时间独立的贡献.
- 该算法生成了一个概率模型,用于区分生物变异和批量效应,并允许细胞在时间上的投射.
主要成果:
- 雪成功地构建了具有生物意义的潜空间,并有效地从scRNA-seq数据中删除了批量效应.
- 该方法产生现实的单细胞水平时间序列,促进对基因表达动态的研究.
- SNOW 增强了对细胞类型特定的昼夜节律的检测,并且可以适应其他时间序列分析.
结论:
- 雪提供了一个强大的计算框架,用于分析复杂的时间过程scRNA-seq数据.
- 该算法克服了集群和伪集群等传统方法的局限性,保留了有价值的单细胞信息.
- 雪有助于更深入地了解时间基因表达模式及其细胞类型特定变异.
相关概念视频
One-Compartment Open Model: Wagner-Nelson and Loo Riegelman Method for ka Estimation
423
This lesson introduces two critical methods in pharmacokinetics, the Wagner-Nelson and Loo-Riegelman methods, used for estimating the absorption rate constant (ka) for drugs administered via non-intravenous routes. The Wagner-Nelson method relates ka to the plasma concentration derived from the slope of a semilog percent unabsorbed time plot. However, it is limited to drugs with one-compartment kinetics and can be impacted by factors like gastrointestinal motility or enzymatic degradation.
On...
On...
423
Noncompartmental Analysis: Mean Residence Time
117
According to statistical moment theory, mean residence time (MRT) is an important measure in pharmacokinetics. MRT can be defined as the expected mean of a probability density function distribution. It provides valuable insights into drug disposition in the body.
After the administration of a drug through intravenous bolus injection, the drug molecules are distributed throughout the body and remain there for varying periods. The MRT represents the average time these drug molecules stay in the...
After the administration of a drug through intravenous bolus injection, the drug molecules are distributed throughout the body and remain there for varying periods. The MRT represents the average time these drug molecules stay in the...
117
Estimating Population Standard Deviation
3.0K
When the population standard deviation is unknown and the sample size is large, the sample standard deviation s is commonly used as a point estimate of σ. However, it can sometimes under or overestimate the population standard deviation. To overcome this drawback, confidence intervals are determined to estimate population parameters and eliminate any calculation bias accurately. However, this only applies to random samples from normally distributed populations. Knowing the sample mean and...
3.0K
Estimating Population Mean with Unknown Standard Deviation
7.6K
In practice, we rarely know the population standard deviation. In the past, when the sample size was large, this did not present a problem to statisticians. They used the sample standard deviation s as an estimate for σ and proceeded as before to calculate a confidence interval with close enough results. However, statisticians ran into problems when the sample size was small. A small sample size caused inaccuracies in the confidence interval.
William S. Gosset (1876–1937) of the...
William S. Gosset (1876–1937) of the...
7.6K
Drug Concentration Versus Time Correlation
672
The plasma drug concentration-time curve is a crucial tool in pharmacokinetics, representing the drug's concentration in plasma at different time intervals post-administration. This curve illustrates the drug's journey from absorption into the systemic circulation, distribution to body tissues, and eventual elimination through excretion or biotransformation.
Two pivotal parameters are the minimum effective concentration (MEC) and the minimum toxic concentration (MTC). The MEC is the...
Two pivotal parameters are the minimum effective concentration (MEC) and the minimum toxic concentration (MTC). The MEC is the...
672
Distributions to Estimate Population Parameter
4.0K
The accurate values of population parameters such as population proportion, population mean, and population standard deviation (or variance) are usually unknown. These are fixed values that can only be estimated from the data collected from the samples. The estimates of each of these parameters are sample proportion, the sample mean, and sample standard deviation (or variance). To obtain the values of these sample statistics, data are required that have particular distribution and central...
4.0K


