Marmal-aid--a database for Infinium HumanMethylation450.

Area of Science:

• Genomics
• Epigenetics
• Bioinformatics

Background:

• DNA methylation is crucial for human genome function and understanding its role in phenotypes.
• Publicly available DNA methylomic data is rapidly expanding, offering research opportunities.
• The Illumina HumanMethylation450 platform is widely used, but data access is challenging due to inconsistent annotation.

Purpose of the Study:

• To introduce Marmal-aid, the first standardized database for DNA methylation.
• To consolidate and re-process publicly available Illumina HumanMethylation450 data.
• To facilitate easier access and analysis of DNA methylation data for researchers.

Main Methods:

• Developed Marmal-aid, a centralized repository for Illumina HumanMethylation450 data.
• Incorporated data normalization and imputation of missing values.
• Provided two access methods: an R package for bioinformaticians and a graphical user interface (GUI) for biologists.

Main Results:

• Marmal-aid is the largest consolidated database of Illumina HumanMethylation450 data.
• The database uses a single, common annotation format for consistency.
• Offers automated data extraction via an R package and visualization tools via a GUI.

Conclusions:

• Marmal-aid simplifies access to and analysis of extensive DNA methylation data.
• It serves as a valuable reference for methylation states across 15 human tissues.
• The database supports integration into existing analysis pipelines and facilitates biological insights.