iMETHYL: an integrative database of human DNA methylation, gene expression, and genomic variation

Komaki, Shohei; Shiwa, Yuh; Furukawa, Ryo; Hachiya, Tsuyoshi; Otomo, Ryo; Satoh, Mamoru; Hitomi, Jiro; Sobue, Kenji; Sasaki, Makoto; Shimizu, Atsushi

doi:10.1038/hgv.2018.8

Cited by 56 publications

(62 citation statements)

References 13 publications

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“…For example, the iMethyl database (http://imethyl.iwate-megabank. org) [56,57] of methylation sites and regulatory effects in peripheral blood mononuclear cells (PBMCs) indicates that this locus is regulatory for the adjacent gene LAMB3 in CD4T cells (effect = 0.0091, p = 4.55 × 10 -5 ). However, both LAMB3 and G0S2 were upregulated in an amyloid β peptide stimulation study of microglia, which suggests that they could be co-regulated [58].…”

Section: Discussionmentioning

confidence: 99%

An epigenome-wide association study of posttraumatic stress disorder in US veterans implicates several new DNA methylation loci

et al. 2020

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Background: Previous studies using candidate gene and genome-wide approaches have identified epigenetic changes in DNA methylation (DNAm) associated with posttraumatic stress disorder (PTSD). Methods: In this study, we performed an EWAS of PTSD in a cohort of Veterans (n = 378 lifetime PTSD cases and 135 controls) from the Translational Research Center for TBI and Stress Disorders (TRACTS) cohort assessed using the Illumina EPIC Methylation BeadChip which assesses DNAm at more than 850,000 sites throughout the genome. Our model included covariates for ancestry, cell heterogeneity, sex, age, and a smoking score based on DNAm at 39 smoking-associated CpGs. We also examined in EPIC-based DNAm data generated from pre-frontal cortex (PFC) tissue from the National PTSD Brain Bank (n = 72).

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Section: Discussionmentioning

confidence: 99%

An epigenome-wide association study of posttraumatic stress disorder in US veterans implicates several new DNA methylation loci

et al. 2020

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“…S7 ). Expression quantitative trait locus (eQTL) analysis using Japanese multi-omics iMETHYL datasets 25 , 32 , 33 showed that the rs8022678 A allele was weakly associated with decreased BCL11B expression level in CD4 + T cells (Supplementary Fig. S8 ).…”

Section: Resultsmentioning

confidence: 99%

“…Previous studies indicated that the 3′- BCL11B gene desert region harbours several remote enhancers that modulate BCL11B gene expression 34 , 35 . Japanese multi-omics iMETHYL datasets 25 , 32 , 33 showed that the rs8022678 A allele was weakly associated with decreased BCL11B expression level in CD4 + T cells. Some variants at the 3′- BCL11B gene desert region were associated with aortic stiffness and cardiovascular disease risk 36 , although rs8022678 was not linked with those variants by linkage disequilibrium ( r 2 = 0.002 in East Asians according to the LDlink server 37 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of polymorphism × sodium interaction effect on blood pressure identifies a novel 3′-BCL11B gene desert locus

Hachiya

Narita

Ohmomo

et al. 2018

Sci Rep

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Excessive sodium intake is a global risk factor for hypertension. Sodium effects on blood pressure vary from person to person; hence, high-risk group targeting based on personal genetic information can play a complementary role to ongoing population preventive approaches to reduce sodium consumption. To identify genetic factors that modulate sodium effects on blood pressure, we conducted a population-based genome-wide interaction analysis in 8,768 Japanese subjects, which was >3 times larger than a similar previous study. We tested 7,135,436 polymorphisms in the discovery cohort, and loci that met suggestive significance were further examined in an independent replication cohort. We found that an interaction between a novel 3′-BCL11B gene desert locus and daily sodium consumption was significantly associated with systolic blood pressure in both discovery and replication cohorts under the recessive model. Further statistical analysis of rs8022678, the sentinel variant of the 3′-BCL11B gene desert locus, showed that differences in mean systolic blood pressure between high and low sodium consumption subgroups were 5.9 mm Hg (P = 8.8 × 10−12) in rs8022678 A carriers and −0.3 mm Hg (P = 0.27) in rs8022678 A non-carriers, suggesting that the rs8022678 genotype can classify persons into sodium-sensitive (A carriers) and sodium-insensitive (A non-carriers) subgroups. Our results implied that rs8022678 A carriers may receive a greater benefit from sodium-lowering interventions than non-carriers.

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“…iMETHYL is an integrative database of human DNA methylation, gene expression, and genomic variation data. It provides cell-type-specific browser tracks (e.g., CD4T, monocytes, and neutrophils) for examining DNA methylation variation, gene expression and single-nucleotide variants in any region of the human genome [25]. These tools are convenient because they provide an interface for representing the results of integrative analyses of methylation and expression data directly from databases.…”

Section: Feature Comparison With Other Bioinformatic Softwarementioning

confidence: 99%

“…ViewBS can correlate between non-CG methylation and gene expression, but the users need to process the data first to allow correlation analyses. MethHC [24] and iMETHYL [25] are databases of methylation and gene expression. They do not allow users to provide their own data, and they can only be applied to specific species.…”

Section: Introductionmentioning

confidence: 99%

MethGET: web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression

Teng

Yen

et al. 2020

BMC Genomics

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Background: DNA methylation is a major epigenetic modification involved in regulating gene expression. The effects of DNA methylation on gene expression differ by genomic location and vary across kingdoms, species and environmental conditions. To identify the functional regulatory roles of DNA methylation, the correlation between DNA methylation changes and alterations in gene expression is crucial. With the advance of next-generation sequencing, genome-wide methylation and gene expression profiling have become feasible. Current bioinformatics tools for investigating such correlation are designed to the assessment of DNA methylation at CG sites. The correlation of non-CG methylation and gene expression is very limited. Some bioinformatics databases allow correlation analysis, but they are limited to specific genomes such as that of humans and do not allow userprovided data. Results: Here, we developed a bioinformatics web tool, MethGET (Methylation and Gene Expression Teller), that is specialized to analyse the association between genome-wide DNA methylation and gene expression. MethGET is the first web tool to which users can supply their own data from any genome. It is also the tool that correlates gene expression with CG, CHG, and CHH methylation based on whole-genome bisulfite sequencing data. MethGET not only reveals the correlation within an individual sample (single-methylome) but also performs comparisons between two groups of samples (multiple-methylomes). For single-methylome analyses, MethGET provides Pearson correlations and ordinal associations to investigate the relationship between DNA methylation and gene expression. It also groups genes with different gene expression levels to view the methylation distribution at specific genomic regions. Multiple-methylome analyses include comparative analyses and heatmap representations between two groups. These functions enable the detailed investigation of the role of DNA methylation in gene regulation. Additionally, we applied MethGET to rice regeneration data and discovered that CHH methylation in the gene body region may play a role in the tissue culture process, which demonstrates the capability of MethGET for use in epigenomic research.

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iMETHYL: an integrative database of human DNA methylation, gene expression, and genomic variation

Cited by 56 publications

References 13 publications

An epigenome-wide association study of posttraumatic stress disorder in US veterans implicates several new DNA methylation loci

An epigenome-wide association study of posttraumatic stress disorder in US veterans implicates several new DNA methylation loci

Genome-wide analysis of polymorphism × sodium interaction effect on blood pressure identifies a novel 3′-BCL11B gene desert locus

MethGET: web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression

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