Accessible Unlicensed Requires Authentication Published by De Gruyter February 29, 2016

A Markov random field-based approach for joint estimation of differentially expressed genes in mouse transcriptome data

Zhixiang Lin, Mingfeng Li, Nenad Sestan and Hongyu Zhao


The statistical methodology developed in this study was motivated by our interest in studying neurodevelopment using the mouse brain RNA-Seq data set, where gene expression levels were measured in multiple layers in the somatosensory cortex across time in both female and male samples. We aim to identify differentially expressed genes between adjacent time points, which may provide insights on the dynamics of brain development. Because of the extremely small sample size (one male and female at each time point), simple marginal analysis may be underpowered. We propose a Markov random field (MRF)-based approach to capitalizing on the between layers similarity, temporal dependency and the similarity between sex. The model parameters are estimated by an efficient EM algorithm with mean field-like approximation. Simulation results and real data analysis suggest that the proposed model improves the power to detect differentially expressed genes than simple marginal analysis. Our method also reveals biologically interesting results in the mouse brain RNA-Seq data set.

Corresponding author: Hongyu Zhao, Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut 06520, USA; and Department of Genetics, Yale School of Medicine, New Haven, Connecticut 06520, USA, e-mail:


We thank Matthew W. State for the financial support of the first author. All computations except that in Figure 4 were performed on the Yale University Biomedical High Performance Computing Center. This study was supported by National Institutes of Health [GM59507, CA154295, MH106934 and NS051869 (N.S.)], and National Science Foundation [DMS 1106738].

Conflict of interest statement: None declared.


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Supplemental Material:

The online version of this article (DOI: 10.1515/sagmb-2015-0070) offers supplementary material, available to authorized users.

Published Online: 2016-2-29
Published in Print: 2016-4-1

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