Thousands of high-quality analyzed methylomes.
The track hub can be turned on for human hg38 with this link.
The track hub file is here:
http://smithlab.usc.edu/trackdata/methylation/hub.txt
You should be able to find it among the public hubs in the list at the UCSC Genome Browser, and if not now, then soon.
There's a chance this hub could be very slow. If you find it useful, and would like to see better performance, the best way to help is simply to let me (Andrew) know, because allocating resources to hardware is only worth it if the resource will be used.
If you would like to suggest a publicly available methylome for inclusion in methbase, please submit an issue here.
The methbase 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 (somewhat arbitrary):
- 0.9: Minimum bisulfite conversion rate.
- 1.0: Minimum average coverage across the genome.
- 0.7: Minimum fraction of CpG sites covered.
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.
These are identified with the hmr command in dnmtools, which is
very similar to the tool I wrote for the Molaro (2011) paper. For
MethBase, the analysis workflows attempt to identify HMRs in every
high-quality methylome from a vertebrate species. This clearly won't
make sense in all cases. In the most extreme example, cells with DNA
methylation erased should not be understood in terms of "valleys" of
low methylation. The approach I plan to implement will be to exclude
HMRs when they seem to be driven by a different biological feature.
This means identifying methylomes that are outliers. So far it seems
like most methylomes with HMRs corresponding to promoters and
enhancers have the following characteristics (which have been evident
for the past 10 years):
- 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.
Eventually I plan to incorporate a sequential identification of PMDs and HMRs so that methylomes with PMDs can still have HMRs accurately identified. This will require revisiting some a fraction of the methylomes to re-run HMR identification.