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Title: ASMdb: A comprehensive database for allele-specific DNA methylation in diverse organisms
Authors: Zhou, Q
Guan, P
Zhu, Z
Cheng, S
Zhou, C
Wang, H
Xu, Q
Sung, WK 
Li, G
Keywords: Alleles
CpG Islands
DNA Methylation
Databases, Genetic
Epigenesis, Genetic
Genomic Imprinting
Polymorphism, Single Nucleotide
X Chromosome Inactivation
Issue Date: 7-Jan-2022
Publisher: Oxford University Press (OUP)
Citation: Zhou, Q, Guan, P, Zhu, Z, Cheng, S, Zhou, C, Wang, H, Xu, Q, Sung, WK, Li, G (2022-01-07). ASMdb: A comprehensive database for allele-specific DNA methylation in diverse organisms. Nucleic Acids Research 50 (D1) : D60-D71. ScholarBank@NUS Repository.
Abstract: DNA methylation is known to be the most stable epigenetic modification and has been extensively studied in relation to cell differentiation, development, X chromosome inactivation and disease. Allele-specific DNA methylation (ASM) is a well-established mechanism for genomic imprinting and regulates imprinted gene expression. Previous studies have confirmed that certain special regions with ASM are susceptible and closely related to human carcinogenesis and plant development. In addition, recent studies have proven ASM to be an effective tumour marker. However, research on the functions of ASM in diseases and development is still extremely scarce. Here, we collected 4400 BS-Seq datasets and 1598 corresponding RNA-Seq datasets from 47 species, including human and mouse, to establish a comprehensive ASM database. We obtained the data on DNA methylation level, ASM and allele-specific expressed genes (ASEGs) and further analysed the ASM/ASEG distribution patterns of these species. In-depth ASM distribution analysis and differential methylation analysis conducted in nine cancer types showed results consistent with the reported changes in ASM in key tumour genes and revealed several potential ASM tumour-related genes. Finally, integrating these results, we constructed the first well-resourced and comprehensive ASM database for 47 species (ASMdb,
Source Title: Nucleic Acids Research
ISSN: 0305-1048
DOI: 10.1093/nar/gkab937
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