Gene profiling for determining pluripotent genes in a time course microarray experiment

DOI10.1093/BIOSTATISTICS/KXN017MaRDI QIDQ3304915zbMATH OpenOpenAlexWikidataFDO

Authors Jonathan Tuke, G. F. V. Glonek, Patricia J. Solomon

Publication date 4 August 2020

Published in Biostatistics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/0805.3598

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10)

Abstract: In microarray experiments, it is often of interest to identify genes which have a pre-specified gene expression profile with respect to time. Methods available in the literature are, however, typically not stringent enough in identifying such genes, particularly when the profile requires equivalence of gene expression levels at certain time points. In this paper, the authors introduce a new methodology, called gene profiling, that uses simultaneous differential and equivalent gene expression level testing to rank genes according to a pre-specified gene expression profile. Gene profiling treats the vector of true gene expression levels as a linear combination of appropriate vectors, i.e., vectors that give the required criteria for the profile. This gene-profile model is fitted to the data and the resultant parameter estimates are summarized in a single test statistic that is then used to rank the genes. The theoretical underpinnings of gene profiling (equivalence testing, intersection-union tests) are discussed in this paper, and the gene profiling methodology is applied to our motivating stem cell experiment.

Recommendations

• On Gene Ranking Using Replicated Microarray Time Course Data
• Identifying differentially expressed genes in unreplicated multiple-treatment microarray timecourse experiments
• A Bayesian Approach to Estimation and Testing in Time-course Microarray Experiments
• A multivariate growth curve model for ranking genes in replicated time course microarray data
• Bayesian models for two-sample time-course microarray experiments

Cites work

• A multivariate empirical Bayes statistic for replicated microarray time course data
• DNA microarray experiments: biological and technological aspects
• Factorial and time course designs for cDNA microarray experiments
• scientific article; zbMATH DE number 1750184 (Why is no real title available?)
• Mixture of linear mixed models for clustering gene expression profiles from repeated microarray experiments
• Multiparameter Hypothesis Testing and Acceptance Sampling

Cited in

(5)

• A multivariate growth curve model for ranking genes in replicated time course microarray data
• Expression profiles of the cell migration-associated genes during rat liver regeneration
• Applying shrinkage variance estimators to the TOST test in high dimensional settings
• Time course analysis of microarray data for the pathway of reproductive development in female rainbow trout
• A Bayesian model to identify multiple expression patterns with simultaneous FDR control for a multi-factor RNA-seq experiment

This page was built for publication: Gene profiling for determining pluripotent genes in a time course microarray experiment

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q3304915)