Purpose of the iMETHYL database

In the last few decades, researchers have elucidated the relationships between genomic variations and phenotypes using genetic linkage analysis and genome-wide association studies (GWAS). Regardless the genomic variation, meanwhile, some studies suggested the relationship between the methylation of CpG dinucleotides and common diseases, and the importance of the epigenetic regulation of DNA methylation has been widely recognized. Although, few open databases for human DNA methylation are available despite the DNA methylation database together with the other omics data will help researchers to dig into the epigenetic mechanism of diseases.

Here, through the iMETHYL genome browser, we aim to provide comprehensive multi-omics data centering on the DNA methylation to serve as a basement or reference for epigenetic researches and so on. We also place importance of cell type-specificity of epigenetic regulation: each cell type has different patterns on DNA methylation, gene expression and resultant relationships between phenotypes that can be obscured by cellular heterogeneity.

Primarily, using the two major immunological blood cell types, CD4T and monocytes isolated from approximately 100 healthy subjects, we performed WGBS, WGS and RNA-Seq based on which we launched the iMETHYL genome browser. Then we added the methylome, genome and transcriptome data obtained from neutrophils to iMETHYL. Using the cell type-specific multi-omics data, we further conducted eQTL, eQTM and mQTL analyses and the results are also available on iMETHYL.

Through providing multi-omics data and QTL information, iMETHYL will serve as a comprehensive reference data and also will help researchers to infer the regulatory mechanisms laying between DNA methylation, genomic variation and gene expression.

Dataset & Citation of iMETHYL

  • Dataset of iMETHYL (for detail, refer to STATISTICS):
    • Summary statistics and distributions of DNA methylation levels of each CpG site of each monocytes, CD4+ T cells, and neutrophils.
    • Average, standard deviation and distributions of gene expression levels of each three cell-types.
    • Allele frequencies for autosomal SNVs.
    • Average DNA methylation levels of 8 cell-populations (CD4+ T cells, CD8+ T cells, B cells, lymphocytes, natural killer cells, PBMC, Leukocyte, monocytes, and neutrophils).
    • Results of QTL analyses (cis-eQTL, eQTM and mQTL).
  • We require that any use of data obtained from our website be cited in your publifications (see below).
    • Iwate Tohoku Medical Megabank Organization, iMETHYL Database; over 100 Japanese whole genome DNA methylation database from monocytes, CD4+ T cells, and neutrophils, (access date), http://imethyl.iwate-megabank.org/
    • T. Hachiya et al. "Genome-wide identification of inter-individually variable DNA methylation sites improves the efficacy of epigenetic association studies" NPJ Genom Med. 2017. 2:11

Public Data Release

  • March 31, 2016. Website was launched. The first data release contained data of SNVs, CpG methylation levels (beta values), and gene expression values (FPKMs) of monocytes and CD4+ T cells from 102 individuals.
  • March 31, 2017. New tracks for neutrophils were added. In addtion, DNAm variability tracks by reference interval, which is defined as the difference between the 95th and 5th percentiles of the DNAm level found among individuals, were added.
  • October 25, 2017. Data of novel SNVs unreported in dbSNP138 were added.
  • March 30, 2018. New tracks for DNA methylation levels of 8 cell-populations, and for results of QTL analyses (cis-eQTL/eQTM/mQTL) were added.

Iwate Tohoku Medical Megabank Organization

  • Iwate Tohoku Medical Megabank Organization (IMM) uses “health” as a tie to bind medical care and areas stricken by disasters. Using health surveys and the creation of a local “biobank”, we are working to enhance and restore medical services, rebuild the community, and create healthy municipalities.
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  • This work was supported by the Tohoku Medical Megabank Project (Special Account for Reconstruction from the Great East Japan Earthquake) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) and Japan Agency for Medical Research and Development (AMED). We thank the members of the Iwate Tohoku Medical Megabank Organization of Iwate Medical University (IMM) and Tohoku Medical Megabank Organization of Tohoku University (ToMMo) for their encouragement and support, as well as the voluntary contributions of all participants. SNV data was provided from Tohoku Medical Megabank Organization of Tohoku University (ToMMo).