MethBase: a reference methylome database

MethBase is a central reference methylome database created from public BS-seq datasets. It contains hundreds of methylomes from well studied organisms. For each methylome, Methbase provides methylation level at individual sites, hypo- or hyper-methylated regions, partially methylated regions, allele-specifically methylated regions, and detailed meta data and summary statistics. These results are generated with the MethPipe software package, a standalone, comprehensive pipeline for analyzing BS-seq data, both WGBS and RRBS.

You may obtain a pdf version of the MethBase Manual for high quality figures.

1  Access MethBase

MethBase is publicly available to the scientific community as a track hub in the UCSC Genome Browser. If you are using the main site of UCSC Genome Browser, the MethBase track hub is built in by default, you may select the MethBase tracks from the Public Hubs section of the UCSC Genome Browser (Figure 1). If you are using the a mirror site of UCSC Genome Browser, you may make the MethBase tracks available by loading the configuration file http://smithlab.usc.edu/trackdata/methylation/hub.txt (Figure 2). Please refer to Using UCSC Genome Browser Track Hubs for how to view unlisted hubs.


Select MethBase public trackhub
Figure 1: Select MethBase hub track from UCSC Genome Browser main site


Add MethBase trackhub in Genome Browser mirros
Figure 2: Add MethBase track hub in mirror sites of UCSC Genome Browser

2  Select tracks for viewing

After you load the MethBase track hub setting file and go to the Genome Browser page, it shows the methylation level tracks and the HMR tracks of typical methylomes (Figure 3A).


Snapshot of HMRs, PMDs, HyperMRs and AMRs
Figure 3: Examples of high-level methylation features available in MethBase through the UCSC Genome Browser track hub: (A) hypo-methylated regions (HMRs); (B) hyper-methylated regions (HyperMRs); (C) partially methylated domains (PMDs), and (D) allele-specific methylated regions (AMRs).

Besides the default methylation tracks and HMR tracks, MethBase also provides a variety of other tracks, including coverage, hyper-methylated regions (Figure 3B), partially methylated domains (Figure 3C) and allele-specific methylated AMRs (Figure 3D). To display those tracks, you may go to the track setting page in one of the three ways: 1) click the project name form the list of projects in Figure 5; 2) right click on of the viewable tracks, and select “Configure track settings” from the manu; or 3) go to the track description page and click the link “Go to track controls”. In the track setting page (Figure 4), you can select additional samples from that project and modify the display settings of more types of data.


Change track display settings
Figure 4: Track setting interface for selectting additional samples and tracks

Below the Browser, you will a list of public methylomes in MethBase under the DNA Methylation section (Figure 5). From the list, you may modify the display settings of several samples from a project.


List of projects and studies acccording to cell types
Figure 5: List of projects available in the MethBase, from the display settings of all tracks from that sample can be modified

3  View meta data and summary statistics

You can click on any track to go to the Description page for that track, which gives detailed meta and summary statistics about that methylome (Figure 6).


MethBase metadata: methylation, coverage, bisulfite conversion rate and higher-level methylation features
Figure 6: Detailed meta data and summary statistics of methylomes

4  Download data for further analysis

There are two ways to download data files from MethBase. First, you may go to the Table Browser to download the data files of any tracks for additional analysis (Figure 7).


Download data with Table Browser
Figure 7: Download data from the Table Browser

Alternatively, you may click the Download link from the Description page of each methylome (Figure 6), which will direct you to the track data directory. The *.meth.bw and *.read.bw files contain methylation level and coverage information respectively at each CpG site. The *.hmr.bb, *.pmd.bb, *.amr.bb files contain HMRs, PMDs and AMRs, and the *.allelic.bw file gives the allelic score at each CpG site. To extract text files from these bigWig and bigBed files, you may use the bigWigToBedGraph and bigBedToBed utilities available from UCSC server.

5  Contact

Please send emails to the methpipe mailing list at methpipe@googlegroups.com if you have any questions, suggestions or comments. Visit MethBase Users Mailing List

6  References

Song Q, Decato B, Hong E, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J, Smith AD (2013) A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. PLOS ONE 8(12): e81148 [PDF] [Publisher Site]


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