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Genome-Wide Analysis of DNA Methylation in Gastrointestinal Cancer
Published on: September 18, 2020
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CanMethdb: a database for genome-wide DNA methylation annotation in cancers
Jianmei Zhao1,2,3, Fengcui Qian1,4,5,6, Xuecang Li3
1The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Hengyang 421001, China.
Bioinformatics (Oxford, England)
|December 8, 2022
Summary
This study introduces CanMethdb, a new database for cancer DNA methylation regulation. It links CpG sites to target genes, including regulatory elements and transcription factor binding sites, aiding cancer research.
Area of Science:
- Genomics
- Epigenetics
- Cancer Biology
Background:
- DNA methylation in gene bodies and promoters is known to affect gene expression in cancer.
- Emerging evidence highlights the role of cytosine-phosphate-guanine (CpG) sites in regulatory elements, influencing transcription factor binding and target gene activation in human cancers.
- There is a critical need for comprehensive resources to map cis-regulatory elements and transcription factor binding sites (TFBS) involved in DNA methylation regulation within cancer.
Purpose of the Study:
- To develop a comprehensive database, CanMethdb, for annotating DNA methylation regulation in cancers.
- To integrate diverse DNA methylation and gene expression data to identify upstream regulatory elements and downstream functional annotations for CpG-gene pairs.
- To provide a user-friendly platform for exploring CpG-target gene associations in various cancer types.
Main Methods:
- Developed CanMethdb (http://meth.liclab.net/CanMethdb/) to store and analyze upstream and downstream annotations for CpG-genes in cancers.
- Integrated extensive DNA methylation and gene expression profiles across 33 TCGA cancer types.
- Implemented query functions based on genomic region, CpG, gene name, or methylation status (hypo/hypermethylated sets).
Main Results:
- CanMethdb contains over 38 million CpG-target gene pairs (6.7 million unique), involving over 385,000 CpGs and 18,000 target genes.
- The database provides annotations for cis-regulatory elements and transcription factors (TFs) for 33 TCGA cancer types.
- Facilitates the study of target gene regulation through DNA methylation in cancer by linking CpGs to genes and regulatory elements.
Conclusions:
- CanMethdb serves as a valuable resource for researchers investigating DNA methylation-driven gene regulation in cancer.
- The database aids in understanding how epigenetic modifications at CpG sites within regulatory elements impact gene expression.
- It supports in-depth biological studies by providing comprehensive annotations and query capabilities for cancer epigenomics.
