CanMethdb

CanMethDB provides genome-wide annotations of DNA methylation, linking CpG sites to cis-regulatory elements, transcription factor-binding sites (TFBS), and target genes to support analysis of gene regulation in cancer.

Key Features:

• Comprehensive annotation: Integrates annotations of upstream cis-regulatory elements, distal regulatory regions, downstream functional annotations of target genes, and transcription factor-binding sites associated with CpG sites.
• Integration of methylation and expression data: Combines DNA methylation profiles with gene expression data to define CpG-target gene relationships.
• Extensive data coverage: Documents 38,986,060 CpG-target gene pairs (6,769,130 unique pairs), 385,217 CpGs, and 18,044 target genes.
• Cancer type specificity: Covers 33 cancer types from The Cancer Genome Atlas (TCGA).
• Hypo- and hypermethylation annotation: Includes annotations distinguishing hypo- and hypermethylated CpG sets.

Scientific Applications:

• Gene regulation analysis: Enables study of gene regulation mechanisms mediated by DNA methylation in cancer.
• Oncogenesis investigation: Facilitates investigation of how DNA methylation changes influence gene expression and contribute to oncogenesis.
• Transcription factor–CpG interaction analysis: Supports analysis of transcription factor interactions with CpG sites and regulatory elements in cancer contexts.

Methodology:

Integrated DNA methylation profiles with gene expression datasets across cancer types and annotated cis-regulatory elements and transcription factor-binding sites associated with CpG sites.