A hidden spatial-temporal Markov random field model for network-based analysis of time course gene expression data
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Publication:2482987
DOI10.1214/07-AOAS145SUPPzbMATH Open1137.62081arXiv0803.3942MaRDI QIDQ2482987FDOQ2482987
Authors: Zhi Wei, Hongzhe Li 
Publication date: 30 April 2008
Published in: The Annals of Applied Statistics (Search for Journal in Brave)
Abstract: Microarray time course (MTC) gene expression data are commonly collected to study the dynamic nature of biological processes. One important problem is to identify genes that show different expression profiles over time and pathways that are perturbed during a given biological process. While methods are available to identify the genes with differential expression levels over time, there is a lack of methods that can incorporate the pathway information in identifying the pathways being modified/activated during a biological process. In this paper we develop a hidden spatial-temporal Markov random field (hstMRF)-based method for identifying genes and subnetworks that are related to biological processes, where the dependency of the differential expression patterns of genes on the networks are modeled over time and over the network of pathways. Simulation studies indicated that the method is quite effective in identifying genes and modified subnetworks and has higher sensitivity than the commonly used procedures that do not use the pathway structure or time dependency information, with similar false discovery rates. Application to a microarray gene expression study of systemic inflammation in humans identified a core set of genes on the KEGG pathways that show clear differential expression patterns over time. In addition, the method confirmed that the TOLL-like signaling pathway plays an important role in immune response to endotoxins.
Full work available at URL: https://arxiv.org/abs/0803.3942
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Cites Work
- Title not available (Why is that?)
- Title not available (Why is that?)
- Exploration, normalization, and summaries of high density oligonucleotide array probe level data
- A hidden spatial-temporal Markov random field model for network-based analysis of time course gene expression data
- Title not available (Why is that?)
- A multivariate empirical Bayes statistic for replicated microarray time course data
- Hidden Markov Models for Microarray Time Course Data in Multiple Biological Conditions
- Functional Hierarchical Models for Identifying Genes with Different Time‐Course Expression Profiles
- Calculating the Statistical Significance of Changes in Pathway Activity From Gene Expression Data
Cited In (26)
- A hidden Markov random field model for genome-wide association studies
- A Bayesian nonparametric mixture model for selecting genes and gene subnetworks
- Using hidden Markov models to model spatial dependence in a network
- Hidden Markov Models for Microarray Time Course Data in Multiple Biological Conditions
- Bayesian modeling of factorial time-course data with applications to a bone aging gene expression study
- Conditional Functional Graphical Models
- Multiple testing for pattern identification, with applications to microarray time-course experiments
- A bi-stable neuronal model of Gibbs distribution
- Incorporating biological information into linear models: a Bayesian approach to the selection of pathways and genes
- The importance of distinct modeling strategies for gene and gene-specific treatment effects in hierarchical models for microarray data
- Nonparametric Functional Graphical Modeling Through Functional Additive Regression Operator
- Large-scale multiple testing under dependence
- A Markov random field-based approach for joint estimation of differentially expressed genes in mouse transcriptome data
- Modeling dependent gene expression
- TGCnA: temporal gene coexpression network analysis using a low-rank plus sparse framework
- Bayesian joint modeling of multiple gene networks and diverse genomic data to identify target genes of a transcription factor
- A binary hidden Markov model on spatial network for amyotrophic lateral sclerosis disease spreading pattern analysis
- High-dimensional functional graphical model structure learning via neighborhood selection approach
- Structured hierarchical models for probabilistic inference from perturbation screening data
- Bayesian hierarchical modeling for signaling pathway inference from single cell interventional data
- A Markov random field-based approach to characterizing human brain development using spatial-temporal transcriptome data
- Bayesian hidden Markov models for dependent large-scale multiple testing
- A hidden spatial-temporal Markov random field model for network-based analysis of time course gene expression data
- Title not available (Why is that?)
- A Bayesian graphical modeling approach to microRNA regulatory network inference
- Rotation gene set testing for longitudinal expression data
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