ASMdb

ASMdb provides a curated repository of allele-specific DNA methylation data and analyses across 47 species to support studies of genomic imprinting, development, and disease.

Key Features:

• Extensive Data Collection: Integration of 4,400 bisulfite sequencing (BS-Seq) datasets and 1,598 corresponding RNA-sequencing (RNA-Seq) datasets from 47 species, including human and mouse.
• Methylation and Allele-Specific Annotation: Computation and reporting of DNA methylation levels, identification of allele-specific methylation (ASM), and cataloging of allele-specific expressed genes (ASEGs).
• Cross-species Distribution Analysis: Characterization of ASM and ASEG distribution patterns across multiple species to enable comparative epigenomic studies.
• Differential Methylation Analysis in Cancer: In-depth differential methylation analyses across nine cancer types highlighting changes in known tumor-related genes and identifying potential ASM-related genes implicated in tumor biology.

Scientific Applications:

• Epigenetic mechanism studies: Enables investigation of allele-specific DNA methylation contributions to gene regulation and epigenetic modulation.
• Genomic imprinting research: Supports identification and characterization of imprinted loci through ASM and ASEG data.
• Cancer biomarker and tumorigenesis research: Facilitates discovery of ASM-associated changes and candidate tumor-related genes across nine cancer types.
• Comparative epigenomics: Allows cross-species comparisons of ASM/ASEG distributions using datasets from 47 species.
• Plant developmental epigenetics: Provides ASM data relevant to studies of plant development and epigenetic regulation.

Methodology:

Analyses were performed on 4,400 BS-Seq and 1,598 RNA-Seq datasets, including computation of DNA methylation levels, identification of allele-specific methylation (ASM) and allele-specific expressed genes (ASEGs), and differential methylation analysis across nine cancer types.