MethBase

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, regions of allele specific methylation, hypo- or hyper-methylated regions, partially methylated regions, and detailed meta data and summary statistics. These results are generated with the MethPipe software package, a standalone, comprehensive pipeline for analyzing bisulfite sequencing data, both WGBS and RRBS. You can obtain a pdf version of the MethBase Manual here.


Demo sessions

The following saved “sessions” pre-load a set of UCSC Genome Browser tracks that showcase some of the data from MethBase that can be viewed in the browser.

Human:

  • Brain: This session shows tracks from brain tissue methylomes and neural progenitors.
  • ESC/iPSC: This session shows a collection of tracks from ESCs and iPSCs. Also included: methylomes for cells that are origins of an iPSC or derived form an iPSC.
  • Blood: This session shows a collection of tracks from multiple blood cells.

Mouse:

  • Reprogramming: This session shows tracks from various stages of mouse male germ cell epigenomic reprogramming.
  • mESCs: This session shows tracks from several mouse ESC methylomes produced by different groups in different projects.

To 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 can select the MethBase tracks from the Public Hubs section of the UCSC Genome Browser:

Select MethBase public trackhub

If you are using the a mirror site of UCSC Genome Browser, you can make the MethBase tracks available by loading the configuration file:


http://smithlab.usc.edu/trackdata/methylation/hub.txt

This is illustrated below. Please refer to Using UCSC Genome Browser Track Hubs for instructions on how to view unlisted hubs. The following shows how to add the MethBase track hub in mirror sites of UCSC Genome Browser:

Add MethBase trackhub in Genome Browser mirros


Select tracks for viewing

After you load the MethBase track hub settings file and go to the Genome Browser page, it shows the methylation level tracks and the HMR tracks of a set of preselected methylomes. Below are examples of high-level methylation features available in MethBase through the UCSC genome browser track hub:

Snapshot of HMRs, PMDs, HyperMRs and AMRs

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

Change track display settings

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

List of projects and studies acccording to cell types


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:

MethBase metadata: methylation, coverage, bisulfite conversion rate and higher-level methylation features


Download data for further analysis

Data can be downloaded for further analysis by clicking the Download link from the Description page of each methylome, 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 can use the bigWigToBedGraph and bigBedToBed utilities available from UCSC server.


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

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]