A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry
| Autor: | Kevin W. Lau, Masako Suzuki, John M. Greally, Reid F. Thompson |
|---|---|
| Rok vydání: | 2009 |
| Předmět: |
Male
Statistics and Probability Computational biology Genome browser Biology Mass spectrometry Polymorphism Single Nucleotide Biochemistry Mass Spectrometry Cell Line Rats Sprague-Dawley Mice chemistry.chemical_compound Animals Sulfites Epigenetics CG-dinucleotide Molecular Biology Genetics Computational Biology Reproducibility of Results Methylation DNA Methylation Original Papers Rats Computer Science Applications Computational Mathematics Restriction enzyme Computational Theory and Mathematics chemistry DNA methylation Dinucleoside Phosphates DNA |
| Zdroj: | Bioinformatics. 25:2164-2170 |
| ISSN: | 1367-4811 1367-4803 |
| DOI: | 10.1093/bioinformatics/btp382 |
| Popis: | Motivation: DNA cytosine methylation is an important epigenetic regulator, critical for mammalian development and the control of gene expression. Numerous techniques using either restriction enzyme or affinity-based approaches have been developed to interrogate cytosine methylation status genome-wide, however these assays must be validated by a more quantitative approach, such as MALDI-TOF mass spectrometry of bisulphite-converted DNA (commercialized as Sequenom's EpiTYPER assay using the MassArray system). Here, we present an R package (‘MassArray’) that assists in assay design and uses the standard Sequenom output file as the input to a pipeline of analyses not available as part of the commercial software. The tools in this package include bisulphite conversion efficiency calculation, sequence polymorphism flagging and visualization tools that combine multiple experimental replicates and create tracks for genome browser viewing. Contact: jgreally@aecom.yu.edu Supplementary information: Supplementary data are available at Bioinformatics online. |
| Databáze: | OpenAIRE |
| Externí odkaz: |
|