The Annals of Applied Statistics

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

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

Full-text: Open access

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.

Article information

Source
Ann. Appl. Stat., Volume 3, Number 4 (2009), 1542-1565.

Dates
First available in Project Euclid: 1 March 2010

Permanent link to this document
https://projecteuclid.org/euclid.aoas/1267453952

Digital Object Identifier
doi:10.1214/09-AOAS258

Mathematical Reviews number (MathSciNet)
MR2752146

Zentralblatt MATH identifier
1185.62186

Keywords
Baculovirus Bernstein polynomials genome-wide expression profile Markov chain Monte Carlo microarray experiments shape restricted regression

Citation

Chien, Li-Chu; Chang, I-Shou; Jiang, Shih Sheng; Gupta, Pramod K.; Wen, Chi-Chung; Wu, Yuh-Jenn; Hsiung, Chao A. Profiling time course expression of virus genes—an illustration of Bayesian inference under shape restrictions. Ann. Appl. Stat. 3 (2009), no. 4, 1542--1565. doi:10.1214/09-AOAS258. https://projecteuclid.org/euclid.aoas/1267453952


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