@inproceedings{0abe9f6ca4204c499ea4f1fcc3bfc64b,
title = "Model-based and context-specific background correction and differential methylation testing for MBDCap-seq",
abstract = "DNA methylation in promoter regions has long been considered an essential mechanism of transcriptional regulation, and it has been demonstrated to be involved in cell development, tumor progression and aging. Methyl-CpG binding domain-based capture followed by high throughput sequencing (MBDCap-seq) is widely used to examine DNA methylation pattern genome-wide. Current MBDCap-seq data analysis approaches focus on measurement of methylated CpG sequence reads, without considering genomic characteristics and tissue-specific context and their impact to the amount of methylated DNA measurement (signal) and background fluctuation (noise). Therefore, specific software needs to be developed to process MBDCap-seq datasets. Here we presented a novel algorithm, termed MBDDiff, implemented as an R package that is designed specifically for processing MBDCap-seq datasets. MBDDiff contains three modules: quality assessment of datasets and quantification of DNA methylation; determination of differential methylation of promoter regions; and visualization functionalities. Simulation studies were carried out to demonstrate the accuracy of MBDDiff algorithm in detecting differential methylation in promoter regions. We also tested functionalities of MBDDiff to a set of in-house prostate cancer samples and a set of public-domain triple negative breast cancer samples profiled with MBDCap-seq protocol, and demonstrated the capability of identifying differential methylation of promoter regions of genes that might contribute to cancer development and progression.",
keywords = "DNA Methylation, Differential methylated regions, Differentially methylation, MBDCap-seq, MBDDiff, XBSeq",
author = "Yuanhang Liu and Desiree Wilson and Leach, {Robin J.} and Yidong Chen",
note = "Publisher Copyright: {\textcopyright} 2015 IEEE.; IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015 ; Conference date: 09-11-2015 Through 12-11-2015",
year = "2015",
month = dec,
day = "16",
doi = "10.1109/BIBM.2015.7359683",
language = "English (US)",
series = "Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015",
publisher = "Institute of Electrical and Electronics Engineers Inc.",
pages = "214--219",
editor = "Schapranow, {lng. Matthieu} and Jiayu Zhou and Hu, {Xiaohua Tony} and Bin Ma and Sanguthevar Rajasekaran and Satoru Miyano and Illhoi Yoo and Brian Pierce and Amarda Shehu and Gombar, {Vijay K.} and Brian Chen and Vinay Pai and Jun Huan",
booktitle = "Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015",
address = "United States",
}