MethBank is a database that integrates whole-genome single-base nucleotide methylomes and provides an interactive browser for visualization of high-resolution DNA methylation data. Here we present an updated implementation of MethBank (http://bigd.big.ac.cn/methbank; Version 2.0) by incorporating high-quality whole-genome bisulfite sequencing methylome maps for five economically important crops (Oryza sativa, Glycine max, Manihot esculenta, Phaseolus vulgaris and Solanum lycopersicum) as well as two model animals (Danio rerio and Mus musculus). Specifically, we collected a large number of methylomes for these species (those are publicly available till May 2016), then excluded low-quality methylomes by primarily considering genome coverage and bisulfite conversion rate, and consequently obtained 90 high-quality methylomes (42 for Oryza sativa, 21 for Glycine max, 1 for Manihot esculenta, 1 for Phaseolus vulgaris, 7 for Solanum lycopersicum, 9 for Danio rerio, and 9 for Mus musculus).
In this updated version, MethBank features genome-wide profiling of methylation distributions across chromosomes, identification of differentially methylated promoters (DMPs) between a range of conditions, and visualization of methylation levels for genes, regions and CpG Islands across multiple different samples. In addition, MethBank incorporates new functionalities to browse and query the data. It provides genome-wide methylation overview and users can retrieve gene methylation profiles and regional methylation levels across all collected samples. MethBank is also equipped with more friendly and intuitive web interfaces to facilitate search of methylation levels for any given gene that is related to DMP or highly methylated CpG islands. Moreover, all related data and processed results are publicly available at http://bigd.big.ac.cn/methbank/downloads. As one of important database resources in BIG Data Center, MethBank will be continuously upgraded and ongoing developments are integration of more high-quality single-base nucleotide methylomes from a wide range of species, with the aim to serve as an important resource for epigenetic studies throughout the world.
MethBank focuses on whole-genome single-base nucleotide methylome data and all raw sequencing data used in MethBank are obtained from NCBI SRA and GSA (http://gsa.big.ac.cn) published before May 2016.
Please see details in the following flowchart.
Remove the adapter sequences of the reads and discard reads whose quality were lower than 20.
WBSA-1.0, BWA (bwa-0.7.10), Samtools (v1.0), R (v2.14.2), Circos (circos-0.69-2), Perl (v5.22.1)
Yes. It is available at http://www.dnamethylome.org
DMP is differentially methylated promoter between two compared samples. To identify DMP, firstly a fisher’s exact test was performed for each promoter region where the average methylation level of one sample is greater, as least 0.1 for C or CH context/0.2 for CG context (delta methylation level), than that of the other sample. For this test, a contingency table was constructed where each row indicated a particular sample and the columns indicated the sum of number of reads that supported a methylated cyosine or an unmethylated cytosine over all the cytosines at this promoter region in a given sample. Secondly, FDR correction (<0.01) for the p-values of fisher’s exact test was used. Finally, the promoter methylation of gene associated with DMP was provided. For plants, DMP were identified in strings of C, CG and CH (H = A, C or T). For animals, only CG sequence context was considered.
E7.5 embryo (Mus musculus), testicle (Danio rerio), cotyledon (Glycine max), leaf (Oryza sativa, Solanum lycopersicum, Manihot esculenta, Phaseolus vulgaris)
Yes. To visualize single-base-resolution DNA methylation data, an interactive and user-friendly methylome browser built on JBrowse is deployed in MethBank. For each species, the methylome browser includes a variety of data tracks and allows users to choose tracks of interest and to zoom and scroll any region along the genome.
In addition, users can change to another species by clicking the name of species on the upper left corner of the Jbrowse.
Yes. MethBank provides downloads of all annotated data via ftp://download.big.ac.cn/methbank/
To support information search and exploration, MethBank provides friendly web interfaces to retrieve diversity information for a specific gene or region. By specifying a gene symbol, users can obtain its methylation states at promoter and gene body, as well as its basic information, gene expression, etc. It should be noted that the promoter region is defined as 2000bp upstream of gene body.
On the search interface, user can learn (i) average methylation levels of promoter and genebody for concerned gene; (ii) promoter methylation levels of genes associated with DMP between different development stages or tissues; (iii) the catalog of genes related to highly methylated CpG Islands.