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

DOI10.1515/SAGMB-2015-0070MaRDI QIDQ306683zbMATH OpenOpenAlexWikidataFDO

Authors Zhixiang Lin, Mingfeng Li, Nenad Sestan, Hongyu Zhao

Publication date 1 September 2016

Published in Statistical Applications in Genetics and Molecular Biology (Search for Journal in Brave)

Full work available at URL http://europepmc.org/articles/pmc5587217

zbMATH Keywords

Markov random field modelneurodevelopmentRNA-seq and differential expression

Mathematics Subject Classification ID

Computational methods in Markov chains (60J22) Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40)

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Cites work

• scientific article; zbMATH DE number 3986503 (Why is no real title available?)
• A Markov random field-based approach to characterizing human brain development using spatial-temporal transcriptome data
• A hidden Markov random field model for genome-wide association studies
• A hidden spatial-temporal Markov random field model for network-based analysis of time course gene expression data
• EM procedures using mean field-like approximations for Markov model-based image segmentation
• Large-Scale Simultaneous Hypothesis Testing
• Quantifying alternative splicing from paired-end RNA-sequencing data
• Small-sample estimation of negative binomial dispersion, with applications to SAGE data
• The mean field theory in EM procedures for Markov random fields

Cited in

(3)

• Homology cluster differential expression analysis for interspecies mRNA-seq experiments
• Detecting differentially expressed genes with RNA-seq data using backward selection to account for the effects of relevant covariates
• A Markov random field-based approach to characterizing human brain development using spatial-temporal transcriptome data

Describes a project that uses

Uses Software

• DAVID
• EBSeq
• RSEM
• DEseq
• casper
• edgeR
• Bioconductor

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