A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. Export

@article{citeulike:5050366, abstract = {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.}, author = {Thompson, Reid F. and Suzuki, Masako and Lau, Kevin W. and Greally, John M.}, citeulike-article-id = {5050366}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp382}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/19561019}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=19561019}, doi = {10.1093/bioinformatics/btp382}, issn = {1460-2059}, journal = {Bioinformatics (Oxford, England)}, keywords = {ms, ocbn, proteomics}, month = {June}, posted-at = {2009-07-03 23:07:48}, priority = {2}, title = {A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry.}, url = {http://dx.doi.org/10.1093/bioinformatics/btp382}, year = {2009} }

TY - JOUR ID - citeulike:5050366 L3 - citeulike-article-id:5050366 N2 - 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. JF - Bioinformatics (Oxford, England) SN - 1460-2059 TI - A pipeline for the quantitative analysis of CG dinucleotide methylation using mass spectrometry. KW - ms KW - ocbn KW - proteomics AU - Thompson, Reid AU - Suzuki, Masako AU - Lau, Kevin AU - Greally, John PY - 2009/06/26/ UR - http://dx.doi.org/10.1093/bioinformatics/btp382 ER -