MACON: a web tool for computing DNA methylation data obtained by the Illumina Infinium Human DNA methylation BeadArray

Epigenomics. 2018 Mar;10(3):249-258. doi: 10.2217/epi-2017-0093. Epub 2018 Jan 18.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line, Tumor
  • Colon / metabolism
  • Colon / pathology
  • Computational Biology / methods*
  • CpG Islands
  • DNA / genetics
  • DNA / metabolism
  • DNA Methylation*
  • Epigenesis, Genetic*
  • Epithelial Cells / metabolism*
  • Epithelial Cells / pathology
  • Gastric Mucosa / metabolism
  • Gastric Mucosa / pathology
  • Genome, Human
  • Humans
  • Molecular Sequence Annotation
  • Oligonucleotide Array Sequence Analysis
  • Software*

Substances

  • DNA