MADA: a web service for analysing DNA methylation array data
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SOFTWARE
Open Access
MADA: a web service for analysing DNA methylation array data Xinyu Hu1, Li Tang1, Linconghua Wang1, Fang-Xiang Wu2 and Min Li1* From 15th International Symposium on Bioinformatics Research and Applications (ISBRA'19) Barcelona, Spain. 3-6 June 2019
* Correspondence: [email protected] 1 School of Computer Science and Engineering, Central South University, Changsha, China Full list of author information is available at the end of the article
Abstract Background: DNA methylation in the human genome is acknowledged to be widely associated with biological processes and complex diseases. The Illumina Infinium methylation arrays have been approved as one of the most efficient and universal technologies to investigate the whole genome changes of methylation patterns. As methylation arrays may still be the dominant method for detecting methylation in the anticipated future, it is crucial to develop a reliable workflow to analysis methylation array data. Results: In this study, we develop a web service MADA for the whole process of methylation arrays data analysis, which includes the steps of a comprehensive differential methylation analysis pipeline: pre-processing (data loading, quality control, data filtering, and normalization), batch effect correction, differential methylation analysis, and downstream analysis. In addition, we provide the visualization of pre-processing, differentially methylated probes or regions, gene ontology, pathway and cluster analysis results. Moreover, a customization function for users to define their own workflow is also provided in MADA. Conclusions: With the analysis of two case studies, we have shown that MADA can complete the whole procedure of methylation array data analysis. MADA provides a graphical user interface and enables users with no computational skills and limited bioinformatics background to carry on complicated methylation array data analysis. The web server is available at: http://120.24.94.89:8080/MADA Keywords: DNA methylation, Normalization, Differential methylation analysis, Downstream analysis
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