Thousands of high-quality uniformly analyzed methylomes.
The UCSC Genome Browser provides visualization for methylomes in MethBase2.
A track hub organized by SRA Study can be turned on for human hg38 with this link.
This track hub URL can be used to load MethBase2 by SRA Study in any UCSC Genome Browser mirror:
http://smithlab.usc.edu/trackdata/methylation/hub.txt
You can also find it among the public hubs in the list at the UCSC Genome Browser.
MethBase2 includes methylomes for the following genomes. 16,223 high-quality methylomes (2026-09-01).
| species | assembly | count |
|---|---|---|
| Mouse | mm39 | 6670 |
| Human | hg38 | 6537 |
| Cow | bosTau9 | 588 |
| Pig | susScr11 | 473 |
| Zebrafish | danRer11 | 339 |
| Chicken | galGal6 | 283 |
| Rhesus | rheMac10 | 270 |
| A. mellifera | apiMel2 | 210 |
| Rat | rn7 | 201 |
| Sheep | oviAri4 | 175 |
| Dog | canFam6 | 145 |
| Stickleback | gasAcu1 | 60 |
| Chimp | panTro6 | 59 |
| Opossum | monDom5 | 44 |
| Crab-eating macaque | macFas5 | 34 |
| Sea hare | aplCal1 | 24 |
| Medaka | oryLat2 | 22 |
| Zebra finch | taeGut2 | 20 |
| X. tropicalis | xenTro10 | 15 |
| Fugu | fr3 | 15 |
| Cat | felCat9 | 9 |
| Gorilla | gorGor6 | 6 |
| S. purpuratus | strPur2 | 4 |
| Rabbit | oryCun2 | 4 |
| Tetraodon | tetNig2 | 3 |
| Panda | ailMel1 | 3 |
| Orangutan | ponAbe3 | 3 |
| Horse | equCab3 | 3 |
| Platypus | ornAna2 | 1 |
| Gibbon | nomLeu3 | 1 |
| Elephant shark | calMil1 | 1 |
| Dolphin | turTru2 | 1 |
If you would like to suggest a publicly available methylome for inclusion, please submit an issue here.
The database includes many more methylomes than are available for viewing with the methbase track hub. Those selected for the track hub meet criteria that help ensure they have been analyzed correctly.
Currently the criteria are:
- 0.9: Minimum bisulfite conversion rate.
- 0.7: Minimum fraction of CpG sites covered.
Assuming a Poisson distribution for the mapped reads (the most conservative assumption here), a fraction of 0.632 of CpG sites covered implies at least a 1x average coverage across the genome. Distributions of mapped reads are never Poisson, so requiring 0.7 of the sites to be covered at least once tends to ensure much deeper average coverage of sites.
Moving forward, not all methylomes will have each kind of "feature" available through the track hub. The criteria are below (in progress). If you want something and you can't find it, possibly those features did not meet criteria. Please contact me to ask and I can check if they might have barely failed to meet the criteria and I might be able to adjust or provide them to you directly.
HMRs are valleys of low methylation in the background of high global methylation
in healthy primary vertebrate methylomes. These are identified with the hmr
command in dnmtools, which is very similar to the tool I wrote for the Molaro
(2011) paper. For MethBase2, the analysis workflow attempts to identify HMRs in
every high-quality methylome from a vertebrate species. These features don't
make sense in all situations. In the most extreme example, cells with DNA
methylation erased should not be understood in terms of "valleys" of low
methylation. Currently the following criteria are used to ensure available sets
of HMRs make sense:
- Human: between 25K and 110K HMRs, with mean size between 750 bp and 4K bp.
- Mouse: between 20K and 100K HMRs, with mean size between 750 bp and 3K bp.
Criteria for other species will be updated here.