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MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data.

Zou D, Sun S, Li R, Liu J, Zhang J, Zhang Z - Nucleic Acids Res. (2014)

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.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.

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Screenshots of the methylome browser in MethBank. (A) Overview of the methylome browser that corresponds to two zebrafish developmental-associated hoxa genes, showing methylation levels, gene expression profiles, DMRs and SNPs. (B) Detailed gene expression information for hoxa13b. (C) Detailed DMR information for hoxa13b. (D) Detailed SNP information for hoxa13b.
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Figure 1: Screenshots of the methylome browser in MethBank. (A) Overview of the methylome browser that corresponds to two zebrafish developmental-associated hoxa genes, showing methylation levels, gene expression profiles, DMRs and SNPs. (B) Detailed gene expression information for hoxa13b. (C) Detailed DMR information for hoxa13b. (D) Detailed SNP information for hoxa13b.

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.


MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data.

Zou D, Sun S, Li R, Liu J, Zhang J, Zhang Z - Nucleic Acids Res. (2014)

Screenshots of the methylome browser in MethBank. (A) Overview of the methylome browser that corresponds to two zebrafish developmental-associated hoxa genes, showing methylation levels, gene expression profiles, DMRs and SNPs. (B) Detailed gene expression information for hoxa13b. (C) Detailed DMR information for hoxa13b. (D) Detailed SNP information for hoxa13b.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4384011&req=5

Figure 1: Screenshots of the methylome browser in MethBank. (A) Overview of the methylome browser that corresponds to two zebrafish developmental-associated hoxa genes, showing methylation levels, gene expression profiles, DMRs and SNPs. (B) Detailed gene expression information for hoxa13b. (C) Detailed DMR information for hoxa13b. (D) Detailed SNP information for hoxa13b.
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.

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.

View Article: PubMed Central - PubMed

Affiliation: CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.

Show MeSH