Allele-Specific DNA Methylation Database
ASMdb: Welcome to Allele-Specific DNA Methylation Database
DNA methylation plays a crucial role in most organisms. Besides, parental alleles in haploids might exhibit different methylation patterns, which can lead to different phenotypes and even different therapeutic and drug responses to diseases. Moreover, related studies have revealed that allele-specific DNA methylation (ASM) can be used as an effective tumor marker and plays important roles in the development of seeds and seedlings. A comprehensive database of high-throughput BS-Seq data and ASM results from multiple species was not available prior to this study.
Here, we constructed the Allele-Specific DNA Methylation Databases (ASMdb), aiming to provide a comprehensive resource and a web tool for showing the DNA methylation level and differential DNA methylation in diverse organisms, including 47 species, such as Homo sapiens, Mus musculus, Arabidopsis thaliana, and Oryza Sativa, with high quality 5998 GEO samples (4400 BS-Seq data and 1598 RNA-Seq data) filted by bisulfite conversion.
The functionalities of Allele-Specific DNA Methylation Database (ASMdb) include the following:
Modules in ASMdb
Zhou Q, Guan P, Zhu Z, Cheng S, Zhou C, Wang H, Xu Q, Sung WK, Li G. ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms. Nucleic Acids Res. 2021 Oct 19:gkab937. doi: 10.1093/nar/gkab937. PMID: 34664666.
Zhou Q, Wang Z, Li J, Sung WK, Li G. MethHaplo: combining allele-specific DNA methylation and SNPs for haplotype region identification. BMC Bioinformatics. 2020 Oct 12;21(1):451. doi: 10.1186/s12859-020-03798-7. PMID: 33045983; PMCID: PMC7552496
Zhou Q, Lim JQ, Sung WK, Li G. An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping. BMC Bioinformatics. 2019 Jan 22;20(1):47. doi: 10.1186/s12859-018-2593-4. PMID: 30669962; PMCID: PMC6343306.
Examples of differential methylation between normal lung tissue and tumor (HOXA5 gene)
Methylation of HOXA5 gene may result in the loss of its expression, and since the encoded protein upregulates the tumor suppressor p53, this protein may play an important role in tumorigenesis. (http://www.cancer-genetics.org/HOXA5.htm); Examples for ASMdb Usage
Statistics of ASMdb Datasets
Information on 47 species, 4400 BS-Seq datasets and 1598 RNA-Seq datasets were downloaded from the GEO. Details about the datasets are provided here.