This track presents DNA methylation data for a wide variety of cell types and tissues as provided by MethBase at the Smith Lab. Methylation signals have a wide variety of genomic functions, including gene expression, cell differentiation, and transposon suppression.
The track selection interface provides a faceted view of the available tracks. The most common facet values are available in selectors on the left edge of the screen, but each column of the table includes a search box to filter for specific data (including partial matches - entering "embryonic" for a filter will match both "embryonic" and "extraembryonic").
Track selection is done via a combination of sample accessions and data types. The main table allows you to select specific sample accessions by checking the box next to their name; the facet selectors make it easier to identify accessions of interest. The three "subtrack types" near the top of the page (reads, levels, and hmr) control which types of data are displayed for the selected accessions.
"Reads" tracks present read counts. "Levels" tracks present an estimate of the percentage of reads covering each site that are methylated. HMR tracks mark hypo-methylated regions, which have unusually low levels of methylation.
Thanks to MethBase and the Smith Lab for use of this data. The track was constructed by Andrew Smith of the Smith Lab, with the assistance of Jonathan Casper of the UCSC Genome Bioinformatics Group.
Song Q, Decato B, Hong EE, Zhou M, Fang F, Qu J, Garvin T, Kessler M, Zhou J, Smith AD. A reference methylome database and analysis pipeline to facilitate integrative and comparative epigenomics. PLoS One. 2013;8(12):e81148. PMID: 24324667; PMC: PMC3855694