MACON: A Web Tool for Computing DNA Methylation Data Obtained By the Illumina Infinium Human DNA Methylation BeadArray

Abstract

Aim: Bioinformatics analysis for Illumina Infinium Human DNA methylation BeadArray is essential, but still remains difficult task for many experimental researchers. We here aimed to develop a browser-accessible bioinformatics tool for analyzing the BeadArray data. Materials & methods: The tool was established as an analytical pipeline using R, Perl and Python programming languages. Results: We introduced a method that groups neighboring probes into a genomic block, which facilitated efficient identification of densely methylated/unmethylated regions. The tool, MACON, provided probe filtering, β-mixture quantile normalization, grouping into genomic blocks, annotation and production of a data subset. Conclusion: MACON allows researchers to analyze the BeadArray data using a web browser (http://epigenome.ncc.go.jp/macon).

Keywords: :

• epigenetics
• microarray
• software

Financial & competing interests disclosure

This research was supported by Practical Research forInnovative Cancer Control from Japan Agency for Medical Research and Development (AMED; grant numbers 16ck0106023h0003 and 17ck0106267h0001). This work was also supported by CREST, JST. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at: www.tandfonline.com/doi/full/10.2217/epi-2017-0093

Additional information

Funding

This research was supported by Practical Research forInnovative Cancer Control from Japan Agency for Medical Research and Development (AMED; grant numbers 16ck0106023h0003 and 17ck0106267h0001). This work was also supported by CREST, JST. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.