MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data.
Bottom Line: DNA methylation plays crucial roles during embryonic development.MethBank allows users to retrieve methylation levels, differentially methylated regions, CpG islands, gene expression profiles and genetic polymorphisms for a specific gene or genomic region.Ongoing efforts are focused on incorporation of methylomes and related data from other organisms.
Affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.Show MeSH
Mentions: To visualize single-base-resolution DNA methylation data, an interactive and user-friendly methylome browser built on JBrowse (23) is deployed in MethBank (Figure 1). For each species, the methylome browser includes a variety of data tracks (namely, CpG island, DMR, gene expression, methylation level, reference gene, reference sequence and SNP) and allows users to choose tracks of interest and to zoom and scroll any region along the genome. Therefore, the methylome browser is of usefulness to investigate methylation status of specific genes/regions across different developmental stages by taking account of multiple relevant data tracks (Figure 1A). Moreover, when clicking a gene/region on a specific track, its corresponding details are displayed and accessible for download (Figure 1B–D). Equipping with the methylome browser, MethBank is able to visualize high-resolution DNA methylation profiles as well as DMRs, gene expression levels, SNPs, CpG islands, etc., in an interactive manner and thus is of great utility to investigate methylation patterns of gametes and early embryos at different developmental stages within specific genes/regions.
Affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.