Assessing genome-wide significance for the detection of differentially methylated regions

DOI10.1515/SAGMB-2017-0050MaRDI QIDQ2324944zbMATH OpenOpenAlexWikidataFDO

Authors Christian M. Page, L. Vos, Trine B. Rounge, Hanne F. Harbo, Bettina K. Andreassen

Publication date 12 September 2019

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

Full work available at URL http://hdl.handle.net/10852/68215

zbMATH Keywords

differentially methylated regionssliding windowgenomics scan statistics

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Biochemistry, molecular biology (92C40) Genetics and epigenetics (92D10)

Recommendations

• HMM-DM: identifying differentially methylated regions using a hidden Markov model
• MethCP: differentially methylated region detection with change point models
• A Bayesian hidden Markov model for detecting differentially methylated regions
• Differential methylation tests of regulatory regions
• A hidden Markov model for identifying differentially methylated sites in bisulfite sequencing data

Cites work

• False discovery rate for scanning statistics
• Probability approximations via the Poisson clumping heuristic
• Scan statistics analysis for detection of introns in time-course tiling array data
• Selection-corrected statistical inference for region detection with high-throughput assays
• Sequential analysis. Tests and confidence intervals
• The statistics of gene mapping

Cited in

(8)

• MethCP: differentially methylated region detection with change point models
• Correcting length-bias in gene set analysis for DNA methylation data
• Differential methylation tests of regulatory regions
• DMRScan
• HMM-DM: identifying differentially methylated regions using a hidden Markov model
• Covariate adjusted differential variability analysis of DNA methylation with propensity score method
• Competitive signal discrimination, methylation reprogramming and genomic imprinting
• An empirical Bayes approach for methylation differentiation at the single nucleotide resolution

Describes a project that uses

Uses Software

• BSmooth
• csaw
• limma
• Bioconductor

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