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

DOI10.1214/14-AOAS802zbMATH Open1454.62352arXiv1506.00480WikidataQ31045903 ScholiaQ31045903MaRDI QIDQ2349587FDOQ2349587

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)

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.

Full work available at URL: https://arxiv.org/abs/1506.00480

Recommendations

• A Markov random field-based approach for joint estimation of differentially expressed genes in mouse transcriptome data
• A hidden spatial-temporal Markov random field model for network-based analysis of time course gene expression data
• Functional Hierarchical Models for Identifying Genes with Different Time‐Course Expression Profiles
• Fréchet estimation of time-varying covariance matrices from sparse data, with application to the regional co-evolution of myelination in the developing brain
• Bayesian spatial transformation models with applications in neuroimaging data

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)

Cites Work

• Title not available (Why is that?)
• Large-Scale Simultaneous Hypothesis Testing
• Title not available (Why is that?)
• A Markov random field-based approach to characterizing human brain development using spatial-temporal transcriptome data
• A hidden spatial-temporal Markov random field model for network-based analysis of time course gene expression data
• A multivariate empirical Bayes statistic for replicated microarray time course data
• Hidden Markov Models for Microarray Time Course Data in Multiple Biological Conditions
• A statistical analysis of memory CD8 T cell differentiation: An application of a hierarchical state space model to a short time course microarray experiment
• Functional Hierarchical Models for Identifying Genes with Different Time‐Course Expression Profiles

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

Uses Software

• DAVID

This page was built for publication: A Markov random field-based approach to characterizing human brain development using spatial-temporal transcriptome data

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q2349587)