A Markov random field-based approach to characterizing human brain development using spatial-temporal transcriptome data

DOI10.1214/14-AOAS802MaRDI QIDQ2349587zbMATH OpenWikidataFDO

Authors Zhixiang Lin, Stephan J. Sanders, Mingfeng Li, Nenad Sestan, Matthew W. State, Hongyu Zhao

Publication date 17 June 2015

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

Full work available at URL https://arxiv.org/abs/1506.00480, https://projecteuclid.org/euclid.aoas/1430226099

zbMATH Keywords

differential expressiongene expressionmicroarrayMarkov random field modelneurodevelopmentMonte Carlo expectation-maximization algorithmspatial and temporal data

Mathematics Subject Classification ID

Random fields; image analysis (62M40) Applications of statistics to biology and medical sciences; meta analysis (62P10)

Abstract: Human neurodevelopment is a highly regulated biological process. In this article, we study the dynamic changes of neurodevelopment through the analysis of human brain microarray data, sampled from 16 brain regions in 15 time periods of neurodevelopment. We develop a two-step inferential procedure to identify expressed and unexpressed genes and to detect differentially expressed genes between adjacent time periods. Markov Random Field (MRF) models are used to efficiently utilize the information embedded in brain region similarity and temporal dependency in our approach. We develop and implement a Monte Carlo expectation-maximization (MCEM) algorithm to estimate the model parameters. Simulation studies suggest that our approach achieves lower misclassification error and potential gain in power compared with models not incorporating spatial similarity and temporal dependency.

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Cites work

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• A Markov random field-based approach to characterizing human brain development using spatial-temporal transcriptome data
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Cited in

(4)

• On Joint Estimation of Gaussian Graphical Models for Spatial and Temporal Data
• A Markov random field-based approach for joint estimation of differentially expressed genes in mouse transcriptome data
• Change-detection-assisted multiple testing for spatiotemporal data
• A Markov random field-based approach to characterizing human brain development using spatial-temporal transcriptome data

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