eQTM Atlas: New Resource Maps DNA Methylation to Gene Expression Across Tissues and Diseases
Researchers have created the eQTM Atlas, a freely available web-based resource cataloging over 11 million associations between DNA methylation sites and gene expression levels across 11 tissue types and 4 disease contexts. The resource addresses a key challenge in epigenome-wide association studies (EWAS) by connecting methylation changes to specific genes rather than relying solely on physical proximity. This tool enables researchers to better interpret how DNA methylation changes affect disease and develop new hypotheses about disease mechanisms.
The eQTM Atlas integrates expression quantitative trait methylation (eQTM) data from eight cohorts, covering 173,886 unique DNA methylation sites and 20,231 genes. While epigenome-wide association studies have identified thousands of methylation sites linked to diseases and traits, interpreting their functional significance has been difficult because researchers typically assigned CpG sites to nearby genes based only on genomic location. The new Atlas solves this by providing statistically validated associations between methylation changes and actual gene expression changes. The web interface allows researchers to search by gene or methylation site, filter by tissue or disease type, visualize results through genome browsers and heatmaps, and download cohort-level data. By connecting disease-associated methylation sites to their functional gene targets, the resource should accelerate the translation of EWAS findings into biological insights and therapeutic targets.
What's missing
The study does not discuss potential limitations of the eQTM approach, such as tissue-specificity of methylation-expression relationships, the possibility of reverse causality (whether methylation changes cause expression changes or vice versa), or how results may vary across different populations or disease stages.
What different sources said
- bioRxivCenter
HOMED enables hierarchical and multimodal optimization of DNA methylation deconvolution across tissues
- bioRxivCenter
eQTM (expression quantitative trait methylation) Atlas: a comprehensive resource of over 11 million DNA methylation-gene expression associations through across 11 tissues and 4 diseases
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