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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Related Experiment Video

Updated: Jun 13, 2026

Targeted DNA Methylation Analysis by Next-generation Sequencing
08:38

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

CpG Atlas: A centralized multi-layer database and AI interface for DNA methylation research.

Jenel F Armstrong1, Shawn Wahi2, Daniel Borrus3

  • 1Program in Computational Biology and Biomedical Informatics, Yale University, New Haven, CT, USA.

Biorxiv : the Preprint Server for Biology
|June 12, 2026
PubMed
Summary
This summary is machine-generated.

CpG Atlas is a new, centralized database that integrates diverse DNA methylation data, including epigenetic clocks and CpG site annotations. This resource streamlines epigenetics research by consolidating fragmented information into an easily queryable framework.

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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer

Published on: September 18, 2020

Area of Science:

  • Epigenetics and Genomics
  • Bioinformatics and Computational Biology
  • Molecular Biology

Background:

  • DNA methylation research has generated extensive data (epigenome-wide association studies, epigenetic clocks, functional annotations) but these resources are fragmented across numerous databases.
  • This fragmentation necessitates significant data cleaning and integration efforts by researchers before meaningful analysis can be performed.
  • A unified, centralized, and easily queryable resource for DNA methylation data is currently lacking.

Purpose of the Study:

  • To present CpG Atlas, a curated relational database designed to integrate diverse DNA methylation data layers.
  • To provide a centralized, scalable, and user-friendly platform for epigenetics research.
  • To facilitate complex multi-dimensional queries and integrative analyses of epigenetic data.

Main Methods:

  • Developed a curated relational database (CpG Atlas) using a snowflake schema and SQL.
  • Integrated 18 distinct annotation layers covering over 1.2 million CpG sites from four generations of Illumina methylation arrays.
  • Consolidated data including CpG-trait associations, Mendelian randomization results, epigenetic clock memberships, array manifest information, probe reliability, and specialized functional annotations.
  • Paired the database with an interactive web tool and a natural language-to-SQL query interface.

Main Results:

  • CpG Atlas integrates over 1.2 million CpG sites and 800,000 CpG-trait associations across multiple annotation layers.
  • The database includes specialized annotations such as solo-WCGW, CoRSIVs, PRC2 binding, transposon/retroelement data, tissue-specific differentially methylated positions, and hallmarks of aging/cancer.
  • Case studies demonstrated CpG Atlas's utility in systematic enrichment analysis of epigenetic clocks and biomarker discovery for Inflammatory Bowel Disease (IBD).

Conclusions:

  • CpG Atlas provides a unified and extensible infrastructure for the epigenetics community, addressing the fragmentation of DNA methylation data.
  • The database facilitates collaborative research, interpretable biomarker development, and integrative analyses.
  • Its scalable design allows for continuous evolution and incorporation of new data, supporting the growing landscape of epigenetic research.