FAQ

1. Introduction

2. Database usage

  • Does MethBank provide a genome browser for visualization of methylation data?

    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 (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.

  • Can I download the data?

    Yes. Please click "Downloads" and choose one of the available species. You will be redirected to data deposited in NCBI GEO database where you can download raw data and processed data.

  • How can I query a gene?

    To support information search and exploration, MethBank provides friendly web interfaces to retrieve a diversity of information for a specific gene or region. By specifying a gene symbol, users can obtain its methylation states at promoter and gene body across multiple developmental stages, as well as its basic information, gene expression, etc.

  • Is it possible to get information about differentially methylated regions (DMRs) associated with a gene?

    Yes. For a given gene symbol or a specified genomic region, MethBank can provide all relevant DMRs between two developmental stages.

  • Can I get DMR information of a region that I concern?

    Yes. Please first click "Search" and then choose one of the available species and click on Go. Second, determine developmental stages and chromosome that you are interested. Finally, after specifying the start site and end site of the region of interest, all DMR information associated with the region can be retrieved.

  • Can I get the average methylation level of a region that I concern?

    Yes. MethBank provides not only the detailed methylation levels for all CG sites in a specific genomic region, but also the averaged methylation level for this region.

  • Is it possible to get SNP information?

    Yes. Detailed SNP information is available for any genomic region,including allele information and genomic locus.

3. Data collection and methods

  • Which versions of genome assemblies are used in MethBank?

    All genome assemblies are downloaded from UCSC database. For Danio rerio genome assembly, UCSC version is danRer7 (Release name is Sanger Institute Zv9). For Mus musculus genome assembly, UCSC version is mm10 (Release name is Genome Reference Consortium GRCm38).

  • What is differentially methylated region (DMR)? How is DMR identified at the genome-wide level?

    DMR is a region that is differentially methylated between two compared samples. To identify the DMR between two samples at the genome-wide level, a similar sliding window approach (Lister et al., 2009) is used to detect regions enriched with differentially methylated sites (DMS). The significance of DMSs between two samples is examined by a two-tailed Fisher's Exact Test, and only cytosines covered at least 10 folds are considered for testing, where P-values are adjusted for multiple testing with the method of Benjamini and Hochberg (Hochberg and Benjamini, 1990). Threshold is selected such that the number of false positive rate is less than 5%. As a result, a region containing at least 5 DMSs and the percentage of DMSs among the CpGs covered 50% is regarded as DMR.

  • How is DMR detected in promoters?

    Promoters are defined as regions 2 kb upstream from TSSs (transcriptional start sites) for each RefGene transcript obtained from UCSC Tables for Mus musculus (mm10). In case of genomic regions with strand information, those on the reverse strand are also oriented from 5' to 3'. Only promoters containing at least 5 CpGs and each CpG site covered by at least five reads are considered for further analysis. The Methylation level of each promoter is determined as the ratio of the number of alignments with C (methylated) over the sum of alignments with C and T for all CpGs in the promoter. Promoters passed two-tailed Fisher's Exact Test (p value < 0.05) are considered as DMR.

4. Terminology

  • Developmental stages in zebrafish.

    After fertilization, sperm penetrate the cellular membrane of egg. The nuclei of both gametes combine and undergo the process of mitosis, resulting in one fertilized zygote. The fertilized zygote sequentially goes though cleavage period, blastula period, gastrula period, segmentation period, pharyngula period, and hatching period. Only early embryo developmental stages are studied in the original study (stages before gastrula period).

    Sperm and Egg are male and female gamete (inbred TU strain), respectively.

    16-cell, 32-cell and 64-cell are the embryos containing 16, 32, and 64 cells, respectively, belonging to cleavage period. There are six cleavages during the cleavage period, transiting from two cells to 64 cells. These transitions during this period occur rapidly and synchronically (the duration of this period is from 0.75 to 2.25 hours). After the first cleavage, the cells, or blastomeres, divide at about 15 minute intervals. The cytoplasmic divisions are meroblastic. They only incompletely undercut the blastodisc, and the blastomeres remain interconnected by cytoplastomic bridges (Kimmel and Law, 1985a).

    128-cell is the embryo containing 128 cells, which is at the early-blastula stage. 1k-cell is the embryo containing 1,000 cells, which is at mid-blastula stage (MBT). The duration of blastula period is from 2.25 to 5.25 hours, transiting from 128 cells to 50% epiboly. During mid-blastula Transition (MBT), the yolk layer forms (YSL), followed by the beginning of epiboly. Epiboly begins in the late blastula (Solnica-Krezel and Driever, 1994), characteristic of the thinning and spreading of both the Yoke Syncytial Layer (YSL) and the blastodisc over the yolk cell.

    Germ ring is the gastrula stage. The duration of this period is from 5.25 to 10.33 hours, transiting from 50% epiboly to 1-4 somites. During the gastrula stage, germ ring (also known as primary germ layers) is produced, including endoderm, mesoderm and ectoderm. When epiboly is complete, the gastrula period ends and the tail bud has form.

    Testis is the organ that produces sperm (from inbred TU strain).

  • Developmental stages in mouse.

    Mouse fetal development sequentially goes through pre-embryonic development, embryonic development (including elongation, gastrulation, and organogenesis), and post-embryonic development. Only early embryo developmental stages are studied in the original study (stages before organogenesis).

    Sperm is the male gamete from mouse strain DBA. Oocyte is the female gamete from mouse strain C57. DBA male mouse and C7 female mouse crossed to produce early stage embryos.

    2cell and 4cell are embryos with 2 and 4 cells, respectively. Both are at cleavage stage.

    ICM is the early inner cell mass, belonging to blastocyst stage, in which there is a distinct inner cell mass and an outer layer of trophectoderm cells.

    E6.5 is the embryo at 6.5 day when earliest heart precursors are 50 founder cells located on both sides of the midline in the epiblast of early gastrula stage embryos.

    E7.5 is the embryo at 7.5 day, belonging to neural plate, presomite stage. The amniotic cavity is sealed off into three distinct cavities; The allantoic bud elongates; The rostral part of the neural plate begins to enlarge to form the head folds. Head folds continue to enlarge and the foregut pocket begins to form.

    E13.5m is the primordial germ cells (PGCs) from male embryo at13.5 day.

    E13.5f is the primordial germ cells (PGCs) from female embryo at 13.5 day.

5. Data and Database Help

  • Comments & Collaborations

    We look forward to worldwide comments, suggestions and guidance from colleagues and peers with common research interests.

    We also invite the scientific community to submit their methylation data to MethBank and to build collaborations in improving the functionalities of MethBank.

  • Contact us

    For any questions or comments, please find our contact information here to contact us.