Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis

Keywords

Methylation, DNA methylation, CpG site, Epigenetics, Computational biology

References

• Array-based DNA methylation profiling in follicular lymphomaCiarán Ó’Riain, Derville O’Shea, Youwen Yang — 2009
• EBV transformation and cell culturing destabilizes DNA methylation in human lymphoblastoid cell lines.Daria Grafodatskaya, Sanaa Choufani, José Carlos Ferreira — 2010
• The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studiesLeming Shi, Wendell Jones, Roderick V. Jensen — 2008
• The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurementsLeming Shi, Leming Shi, Laura Reid — 2006
• CpG island hypermethylation and tumor suppressor genes: a booming present, a brighter futureManel Esteller — 2002
• Rat toxicogenomic study reveals analytical consistency across microarray platformsLei Guo, Edward K. Lobenhofer, Charles Wang — 2006
• Gene silencing in cancer in association with promoter hypermethylation.James G. Herman, Stephen B. Baylin — 2003
• Principles and challenges of genome-wide DNA methylation analysisPeter W. Laird — 2010
• Genome-wide DNA methylation analysis of archival formalin-fixed paraffin-embedded tissue using the Illumina Infinium HumanMethylation27 BeadChip.Christina Thirlwell, Marianne Eymard, Andrew Feber — 2010
• lumi: a pipeline for processing Illumina microarrayPan Du, Warren A. Kibbe, Simon Lin — 2008
• Comprehensive high-throughput arrays for relative methylation (CHARM).Rafael A. Irizarry, Christine Ladd‐Acosta, Benilton S. Carvalho — 2008
• Experimental comparison and cross-validation of the Affymetrix and Illumina gene expression analysis platformsMichael Barnes — 2005
• Effects of dependence in high-dimensional multiple testing problemsKyung In Kim, Mark A. van de Wiel — 2008
• Genome-Wide Profiling of DNA Methylation Reveals a Class of Normally Methylated CpG Island PromotersLanlan Shen, Yutaka Kondo, Yi Guo — 2007
• Prenatal tobacco smoke exposure affects global and gene-specific DNA methylation.Carrie V. Breton, Hyang‐Min Byun, Madé Wenten — 2009
• A variance-stabilizing transformation for gene-expression microarray dataBlythe Durbin, J.S. Hardin, Douglas M. Hawkins — 2002
• High-throughput DNA methylation profiling using universal bead arrays.Marina Bibikova, Zhenwu Lin, Lixin Zhou — 2006
• Model-based variance-stabilizing transformation for Illumina microarray dataSimon Lin, Pan Du, Wolfgang Huber — 2008
• Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitusChristopher G. Bell, Andrew E. Teschendorff, Vardhman K. Rakyan — 2010
• GoldenGate assay for DNA methylation profiling.Marina Bibikova, Jian‐Bing Fan — 2009

Cited by

• DNA methylation profiling of well‐differentiated thyroid cancer uncovers markers of recurrence free survivalН. М. Межевич, А. А. Жабрев — 2014
• Tumor subtype-specific cancer-testis antigens as potential biomarkers and immunotherapeutic targets for cancersЕрмолаев Серафим Николаевич — 2013
• Methylome sequencing in triple-negative breast cancer reveals distinct methylation clusters with prognostic valueMartínez Vázquez, Leonor Esther — 2015
• Identification of Novel Gene Targets and Putative Regulators of Arsenic-Associated DNA Methylation in Human Urothelial Cells and Bladder CancerEdoardo Roberto Barbieri — 2015
• Transcriptional similarity in couples reveals the impact of shared environment and lifestyle on gene regulation through modified cytosines保子 尾崎 — 2016
• Epigenetic Contribution of the Myosin Light Chain Kinase Gene to the Risk for Acute Respiratory Distress SyndromeCarsten Herresthal — 2016
• Novel miRNA-mRNA interactions conserved in essential cancer pathways良丙 森永, 安弘 延藤 — 2017
• Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc孜 竹崎 — 2017
• Social and physical environments early in development predict DNA methylation of inflammatory genes in young adulthoodPanjaitan, Martaida — 2017
• Epigenetic dysregulation in adrenocortical carcinoma, a systematic review of the literature.Vladimir Mejia Ayala — 2017
• Epigenetics of Delirium and Aging: Potential Role of DNA Methylation Change on Cytokine Genes in Glia and Blood Along With AgingVaibhav Gandhi, Girijesh Prasad, Damien Coyle — 2018
• Differential regulation of CpG island methylation within divergent and unidirectional promoters in colorectal cancerGemma Tejedor Papell — 2019
• Unraveling the Role of Epigenetics in Aging and Chronic Disease.Alicia L. Zagel — 2013
• ROLE OF ALLERGIC SENSITIZATION, FILAGGRIN VARIANTS, AND DNAAli H. Ziyab — 2014
• The association of DNA methylation patterns in TCF7L2 and GIPR genes with Type 2 DiabetesSílvia Canivell — 2014
• The Effect of High-intensity Interval Training on Maximal Aerobic Capacity, DNA Methylation and Gene Expression in Healthy Elderly MenKine Andenæs — 2013
• Determination of DNA methylation levels using Illumina HumanMethylation450 BeadChips.Melanie A. Carless — 2015
• Computational analysis of CpG site DNA methylationMohammadmersad Ghorbani — 2013
• Genetic-epigenetic interactions in medulloblastoma developmentDolores Mary Hamilton — 2014
• Methods for integrative analysis of genomic dataPaul T. Manser — 2014

Related papers

• Genetic and environmental impacts on DNA methylation levels in twins.İdil Yet, Pei-Chien Tsai, Juan Castillo‐Fernandez — 2016
• DNA methylation in osteoarthritic chondrocytes: a new molecular target.H.I. Roach, Thomas Aigner — 2007
• Early Nutritional Influences on Human Developmental Epigenetics.Robert A. Waterland — 2015
• Changes of DNA methylation of Isoetes sinensis under Pb and Cd stressGuohua Ding, Dan-Di Guo, Yang Guan — 2018
• Methylation of CpG sites in BCL2 major breakpoint region and the increase of BCL2/JH translocation with agingIdoia Martín‐Guerrero, Elena de Prado, Maite Ardanaz — 2015
• Distribution of DNA methylation, CpGs, and CpG islands in human isochores.Annalisa Varriale, Giorgio Bernardi — 2010
• Global methylation profiles in DNA from different blood cell typesHui‐Chen Wu, Lissette Delgado‐Cruzata, Julie D. Flom — 2011
• Effects of Particulate Matter on Genomic DNA Methylation Content and iNOS Promoter MethylationLetizia Tarantini, Matteo Bonzini, Pietro Apostoli — 2008
• Progressive age-dependent DNA methylation changes start before adulthood in mouse tissues.Masaki Takasugi — 2011