Literature DB >> 19488875

Methylation analysis by microarray.

Daniel E Deatherage1, Dustin Potter, Pearlly S Yan, Tim H-M Huang, Shili Lin.   

Abstract

Differential methylation hybridization (DMH) is a high-throughput DNA methylation screening tool that utilizes methylation-sensitive restriction enzymes to profile methylated fragments by hybridizing them to a CpG island microarray. This array contains probes spanning all the 27,800 islands annotated in the UCSC Genome Browser. Herein we describe a DMH protocol with clearly identified quality control points. In this manner, samples that are unlikely to provide good read-outs for differential methylation profiles between the test and the control samples will be identified and repeated with appropriate modifications. The step-by-step laboratory DMH protocol is described. In addition, we provide descriptions regarding DMH data analysis, including image quantification, background correction, and statistical procedures for both exploratory analysis and more formal inferences. Issues regarding quality control are addressed as well.

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Year:  2009        PMID： 19488875      PMCID： PMC2838393          DOI： 10.1007/978-1-60327-192-9_9

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  18 in total

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2.  Assessing gene significance from cDNA microarray expression data via mixed models.

Authors:  R D Wolfinger; G Gibson; E D Wolfinger; L Bennett; H Hamadeh; P Bushel; C Afshari; R S Paules
Journal:  J Comput Biol       Date:  2001       Impact factor: 1.479

3.  Missing value estimation methods for DNA microarrays.

Authors:  O Troyanskaya; M Cantor; G Sherlock; P Brown; T Hastie; R Tibshirani; D Botstein; R B Altman
Journal:  Bioinformatics       Date:  2001-06       Impact factor: 6.937

4.  Statistical issues in cDNA microarray data analysis.

Authors:  Gordon K Smyth; Yee Hwa Yang; Terry Speed
Journal:  Methods Mol Biol       Date:  2003

5.  A comparison of normalization methods for high density oligonucleotide array data based on variance and bias.

Authors:  B M Bolstad; R A Irizarry; M Astrand; T P Speed
Journal:  Bioinformatics       Date:  2003-01-22       Impact factor: 6.937

6.  Differential methylation hybridization: profiling DNA methylation with a high-density CpG island microarray.

Authors:  Pearlly S Yan; Dustin Potter; Daniel E Deatherage; Tim H-M Huang; Shili Lin
Journal:  Methods Mol Biol       Date:  2009

7.  Computational identification of promoters and first exons in the human genome.

Authors:  R V Davuluri; I Grosse; M Q Zhang
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

8.  Comprehensive analysis of CpG islands in human chromosomes 21 and 22.

Authors:  Daiya Takai; Peter A Jones
Journal:  Proc Natl Acad Sci U S A       Date:  2002-03-12       Impact factor: 11.205

9.  Effects of atmospheric ozone on microarray data quality.

Authors:  Thomas L Fare; Ernest M Coffey; Hongyue Dai; Yudong D He; Deborah A Kessler; Kristopher A Kilian; John E Koch; Eric LeProust; Matthew J Marton; Michael R Meyer; Roland B Stoughton; George Y Tokiwa; Yanqun Wang
Journal:  Anal Chem       Date:  2003-09-01       Impact factor: 6.986

10.  Normalization and analysis of DNA microarray data by self-consistency and local regression.

Authors:  Thomas B Kepler; Lynn Crosby; Kevin T Morgan
Journal:  Genome Biol       Date:  2002-06-28       Impact factor: 13.583
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  6 in total

1.  Hypermethylation of the gene LARP2 for noninvasive prenatal diagnosis of β-thalassemia based on DNA methylation profile.

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Review 2.  Guidelines for the design, analysis and interpretation of 'omics' data: focus on human endometrium.

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Journal:  Hum Reprod Update       Date:  2013-09-29       Impact factor: 15.610

3.  Statistical challenges in analyzing methylation and long-range chromosomal interaction data.

Authors:  Zhaohui Qin; Ben Li; Karen N Conneely; Hao Wu; Ming Hu; Deepak Ayyala; Yongseok Park; Victor X Jin; Fangyuan Zhang; Han Zhang; Li Li; Shili Lin
Journal:  Stat Biosci       Date:  2016-03-07

Review 4.  Profiling DNA methylomes from microarray to genome-scale sequencing.

Authors:  Yi-Wei Huang; Tim H-M Huang; Li-Shu Wang
Journal:  Technol Cancer Res Treat       Date:  2010-04

5.  The MethDet: a technology for biomarker development.

Authors:  Victor V Levenson; Anatoliy A Melnikov
Journal:  Expert Rev Mol Diagn       Date:  2011-11       Impact factor: 5.225

6.  BCurve: Bayesian Curve Credible Bands Approach for the Detection of Differentially Methylated Regions.

Authors:  Chenggong Han; Jincheol Park; Shili Lin
Journal:  Methods Mol Biol       Date:  2022
  6 in total

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