Profiling time course expression of virus genes -- an illustration of Bayesian inference under shape restrictions

DOI10.1214/09-AOAS258zbMATH Open1185.62186arXiv1009.5785OpenAlexW3102035607MaRDI QIDQ965124FDOQ965124

Authors: Li-Chu Chien, Shih Sheng Jiang, Chi-Chung Wen, Yuh-Jenn Wu, Chao A. Hsiung, I-Shou Chang, P. K. Gupta 

Publication date: 21 April 2010

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: There have been several studies of the genome-wide temporal transcriptional program of viruses, based on microarray experiments, which are generally useful in the construction of gene regulation network. It seems that biological interpretations in these studies are directly based on the normalized data and some crude statistics, which provide rough estimates of limited features of the profile and may incur biases. This paper introduces a hierarchical Bayesian shape restricted regression method for making inference on the time course expression of virus genes. Estimates of many salient features of the expression profile like onset time, inflection point, maximum value, time to maximum value, area under curve, etc. can be obtained immediately by this method. Applying this method to a baculovirus microarray time course expression data set, we indicate that many biological questions can be formulated quantitatively and we are able to offer insights into the baculovirus biology.

Full work available at URL: https://arxiv.org/abs/1009.5785

Recommendations

• A Bayesian Approach to Estimation and Testing in Time-course Microarray Experiments
• Bayesian models for two-sample time-course microarray experiments
• Flexible temporal expression profile modelling using the Gaussian process
• Predicting viral infection from high-dimensional biomarker trajectories
• A Quantitative Study of Gene Regulation Involved in the Immune Response of Anopheline Mosquitoes

zbMATH Keywords

Markov chain Monte CarloBernstein polynomialsbaculovirusmicroarray experimentsgenome-wide expression profileshape restricted regression

Mathematics Subject Classification ID

Bayesian inference (62F15) Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40) Systems biology, networks (92C42)

Cites Work

• A simple nonparametric estimator of a strictly monotone regression function
• Title not available (Why is that?)
• Random Bernstein Polynomials
• Bayesian Survival Analysis Using Bernstein Polynomials
• Bayes Factors
• A Bayesian Formulation of Exploratory Data Analysis and Goodness‐of‐fit Testing*
• Bayesian Semiparametric Isotonic Regression for Count Data
• Maximum Likelihood Estimates of Monotone Parameters
• Title not available (Why is that?)
• Point Estimates of Ordinates of Concave Functions
• A nonparametric Bayes method for isotonic regression
• Estimating and depicting the structure of a distribution of random functions
• Comparing the shapes of regression functions
• Title not available (Why is that?)
• A note on the consistency in Bayesian shape-restricted regression with random Bernstein polynomials
• Profiling time course expression of virus genes -- an illustration of Bayesian inference under shape restrictions

Cited In (4)

• A Quantitative Study of Gene Regulation Involved in the Immune Response of Anopheline Mosquitoes
• Profiling time course expression of virus genes -- an illustration of Bayesian inference under shape restrictions
• Predicting viral infection from high-dimensional biomarker trajectories
• A variable selection approach to monotonic regression with Bernstein polynomials

Uses Software

• BayesDA

This page was built for publication: Profiling time course expression of virus genes -- an illustration of Bayesian inference under shape restrictions

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q965124)