The eQTM Atlas

Home Page Overview

Overview of the eQTM Atlas interface and navigation.

Welcome to the eQTM Atlas.

Expression quantitative trait methylation (eQTM) analysis attempts to identify CpG sites that connect methylation-related associations with gene expression of cis (close by) or trans (far away) genes. The eQTM Atlas provides rich data, informative genome maps, and other pertinent information about eQTM genes that are significantly associated with various CpGs, some of which may have regulatory effects on gene expression. Our database is also linked to the EWAS Atlas, enabling cross-referencing of two powerful resources for methylation data.

Examples: PDCD10 , USP6 , cg04983687 , cg00119778

Gene ↔ CpG Usage Guide

How to navigate gene- and CpG-centric searches and interpret eQTM results.
Download Results

Genome Browser Usage Guide

How to explore genomic context, tracks, and loci in the eQTM Genome Browser.

This page lets you view eQTMs and CpGs in the context of their genomic locations. Search by gene name or CpG probe ID. You can filter by cohort or by disease.

Heatmap Usage Guide

How to interpret and customize heatmaps across tissues, cohorts, and features.

This page lets you view a heatmap of p-values for data points across various tissues. Scroll to the right of the heatmap to view the legend and other plot controls.

EWAS–eQTM Usage Guide

How to interpret EWAS-linked eQTM associations and cohort-level summaries.

This page lets you view EWAS Atlas associations in tandem with our eQTM database cohort data.

Help and Documentation

Using the eQTM Atlas

The eQTM Atlas helps researchers move from CpG sites or genes to tissue-aware DNA methylation-gene expression associations, then connect those CpGs to EWAS traits when useful.

1. Overview

Expression quantitative trait methylation, or eQTM, analysis identifies CpG sites whose DNA methylation levels are associated with gene expression. In addition, these associations can help connect methylation findings from EWAS to candidate regulatory genes, including genes that are not simply the nearest annotated gene. The Atlas can be queried in two ways: users can search by a DNAm CpG site to identify associated genes, or search by a gene to identify associated CpG sites.

>11M
curated eQTM associations
173,886
unique CpG probes
20,231
unique genes
11
tissue types represented

2. Data Content

The Atlas integrates summary-level eQTM results from multiple human cohorts and tissue contexts. The database includes both cis- and trans-eQTM associations, disease and tissue labels, CpG and gene genomic coordinates, effect estimates, P values, and FDR values where available.

CpG probe
A measured DNA methylation site, usually represented by a probe ID such as cg05575921.
eQTM gene
A gene whose expression is statistically associated with methylation at a CpG site.
cis-eQTM
An association where the CpG and gene are nearby, typically within 1 Mb of the transcription start site.
trans-eQTM
An association where the CpG and gene are farther apart, either on the same chromosome or on different chromosomes.
Tip: eQTM signals can be tissue-specific. When possible, compare results across tissues and cohorts before prioritizing candidate CpG-gene pairs.

4. EWAS-eQTM Integration

The EWAS-eQTM Integration tab connects CpGs from the EWAS Atlas with genes from the eQTM Atlas. This supports a data-driven alternative to relying only on nearby or promoter/body gene annotations.

  1. Enter a CpG ID in the CpG search field.
  2. Optionally choose an EWAS trait keyword and EWAS tissue.
  3. Select an eQTM cohort. This field is required because eQTM associations are cohort- and tissue-dependent.
  4. Review the combined EWAS and eQTM results table, including EWAS traits, study IDs, eQTM genes, tissues, P values, and FDR values.

Open the EWAS Atlas

5. Interpreting Results

P value
Statistical evidence for an association between CpG methylation and gene expression.
FDR
Multiple-testing adjusted significance value when reported by the source study.
Beta
Estimated direction and magnitude of the CpG-gene expression association.
-log10(P)
A transformed significance scale used in plots and heatmaps; larger values indicate stronger evidence.
Important: an eQTM association suggests a methylation-expression relationship, but it does not by itself prove causality. Biological interpretation should consider tissue, cohort, study design, effect direction, and external evidence.

6. Downloads and Data Upload

Use the Downloads tab to retrieve cohort-level eQTM summary statistics. Search-result tables also include download buttons when results are available.

  • Downloaded files are intended for downstream analyses such as pathway enrichment, gene-set enrichment, or cross-study comparison.
  • Investigators can contact the eQTM Atlas team to discuss adding tissue-labeled eQTM datasets to the resource.
  • Common upload formats include csv, tsv, txt, FASTQ, and BAM, depending on the data type and transfer agreement.

7. Citation and Contact

If you use the eQTM Atlas in your research, please cite the eQTM Atlas manuscript when available and cite the original source studies for cohort-specific results.

eQTM Atlas web app | Source code

Questions, issues, or data upload inquiries: ads303@pitt.edu